https://www.na-mic.org/w/api.php?action=feedcontributions&user=Agouaillard&feedformat=atomNAMIC Wiki - User contributions [en]2024-03-19T02:02:49ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=2011_Summer_Project_Week_DICOM_RT&diff=688332011 Summer Project Week DICOM RT2011-06-21T13:58:41Z<p>Agouaillard: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
[[Image:wiki_noise.png|190px|Synthetic noise]]<br />
[[Image:wiki2.png|108px|Synthetic CT]]<br />
[[Image:wiki3.png|108px|Synthetic labelmap]]<br />
[[Image:wiki4.png|300px|Synthetic dose]]<br />
<br />
<br />
<br />
<br />
==Key Investigators==<br />
* MGH: Nadya Shusharina, Greg Sharp<br />
* Kitware: Luis Ibanez<br />
* Isomics: Steve Pieper<br />
* Cosmo software: Drew Wassem<br />
* A*STAR: Alexandre GOUAILLARD (in spirit)<br />
<br />
'''Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK'''<br />
<br />
Figure out the best representation in ITK and Slicer4 for various RT and related datastructures.<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
We are designing synthetic DICOM-RT dataset which includes CT image, structure set and dose distribution. The following guidelines are used. We measured the noise power spectrum of a real CT image and constructed synthetic image with exactly the same spectrum. Then we included "skin" and one internal spherical structure. Synthetic contours were generated and recorded in labelmap format. Synthetic dose distribution was generated in mha format. <br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
Currently synthetic DICOM-RT is loaded into Slicer 3.6.3 from file through Plastimatch extension DICOM/DICOM-RT Import. We plan to build Plastimatch command line module that will allow us to create synthetic image, structures and dose distribution interactively according to user's needs. <br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==References==<br />
<br />
* [http://support.dcmtk.org/docs-dcmrt/mod_dcmrt.html DCMRT from Oldenberg/Offis/DCMTK and DKFZ in Heidelberg]<br />
* [http://plastimatch.org/ Plastimatch]<br />
* [http://www.itk.org/Wiki/ITK_Release_4/DICOM ITKv4 DICOM]<br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NAMIC Kit as a <br />
<br />
#NITRIC distribution<br />
#Slicer Module<br />
##Built-in: perhaps RT support can become part of MRML<br />
##Extension -- commandline: Maybe, if needed<br />
##Extension -- loadable: yes, for a custom interface</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=Microscopy_Image_Analysis&diff=66991Microscopy Image Analysis2011-05-04T16:22:52Z<p>Agouaillard: /* Schedule */</p>
<hr />
<div>= Open Workshop on Microscopy Image Analysis in ITK and VTK =<br />
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK<br />
<br />
== Preparation ==<br />
If you would like to participate in this workshop then please:<br />
* Add your name to the "Participants" section below<br />
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page<br />
* Register for the overall conference from [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here]<br />
* Create a wiki page describing your project following the preparation instructions on the [[2010_Summer_Project_Week#Preparation]] home page and link this to your project listing<br />
<br />
== Background ==<br />
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.<br />
<br />
== Focus ==<br />
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.<br />
<br />
==Format==<br />
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.<br />
<br />
== Schedule ==<br />
* Monday afternoon- 1 slide lightning talk of project planned for the week using your project page<br />
* Wednesday afternoon - Microscopy Breakout Session ( Location: [http://whereis.mit.edu/?go=32 Kiva])<br />
** 1:00pm - 2:20pm: Current efforts (20 minute talks per lab). The goal is to describe the user application you are focussed on, your software approach (demos of software are great), and how others can interface with your efforts.<br />
*** 1:00pm: Megason Lab- Dept of Systems Biology, Harvard<br />
**** Sean Megason - Microscopy image analysis for into imaging of embryogenesis<br />
**** Lydie Souhait - Demo of GoFigure<br />
**** Arnaud Gelas - Interfacing with the Megason Lab<br />
*** 1:20pm: Machiraju Lab- Ohio State Univ<br />
**** Shantanu Singh - Large Scale Analysis of Cellular Phenotypes in the Tumor Microenvironment<br />
**** Liya Ding - Image Analysis of Large Histology Datasets using ITK<br />
*** 1:40pm: Palaniappan Lab- Univ of Missouri<br />
*** 2:00pm: Roysam Lab- Rensselaer Polytechnic Institute<br />
*** 2:20pm: Gouaillard Lab - Singapore Immunology Network<br />
*** 2:40pm: Carolina Wahlby - Broad Institute<br />
** 2:45pm: Roundtable discussion of standards/interfaces<br />
*** Image file types<br />
*** Input-output interface for segmentation and tracking filters <br />
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type) <br />
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?<br />
*** Common human tasks<br />
**** Manual segmentation and editing of results<br />
**** Visualization of results<br />
** Future directions<br />
* Friday- 1 slide summary of results for the week using your project page<br />
* The rest of the time will be spent coding on projects<br />
<br />
== Projects ==<br />
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page<br />
<br />
== Participants ==<br />
Please add your name to the list if you are interested in participating in this workshop<br />
# Raghu Machiraju, Ohio State University<br />
# Thierry Pecot, Ohio State University<br />
# Shantanu Singh, Ohio State University<br />
# Liya Ding, Ohio State University<br />
# Kannappan Palaniappan, University of Missouri<br />
# Ilker Ersoy, University of Missouri<br />
# Adel Hafiane, ENSI-Bourges, France<br />
# Yousef Al-Kofahi, Rensselaer Polytechnic Institute, CompuCyte Corporation<br />
# Kedar Grama, Rensselaer Polytechnic Institute<br />
# Raghav Padmanabhan, Rensselaer Polytechnic Institute<br />
# Arnaud Gelas, Harvard Medical School<br />
# Kishore Mosaliganti, Harvard Medical School<br />
# Nicolas Rannou, Harvard Medical School<br />
# Antonin Perrot-Audet, Harvard Medical School<br />
# Lydie Souhait, Harvard Medical School<br />
# Sean Megason, Harvard Medical School<br />
# Luis Ibanez, Kitware<br />
# Andinet Enquobahrie, Kitware<br />
# Mathieu Malaterre, CoSMo<br />
# Alex. Gouaillard. A*STAR / CoSMo<br />
# Sonia Pujol. Brigham and Women's Hospital<br />
# Steve Pieper, Isomics, Inc.<br />
# Alex Yarmarkovich, Isomics, Inc.<br />
# Curtis Lisle, KnowledgeVis<br />
# Tammy Riklin Raviv, CSAIL, MIT<br />
# Marc Niethammer, UNC Chapel Hill<br />
# Carolina Wahlby, Broad Institute</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=AHM_2011&diff=66989AHM 20112011-05-04T16:17:52Z<p>Agouaillard: /* Registered Attendees */</p>
<hr />
<div> Back to [[Events]]<br />
[[Image:PW-SLC2011.png|300px]]<br />
<br />
January 10-14, 2011, Salt Lake City, Utah<br />
== Introduction ==<br />
{| border="00" cellpadding="8" cellspacing="0"<br />
|-<br />
| rowspan="2" align="left" | '''This is the home page for the 2011 NA-MIC all hands meeting (AHM).''' NA-MIC participants meet for a AHM once a year. The purpose of the AHM is to coordinate, discuss plans and report to NIH officers and the external advisory board (EAB). The external advisory board meets with the NA-MIC leadership immediately after the AHM. In parallel, NA-MIC is organizing a project week. These events, with the exception of the EAB meeting, are open to collaborators and potential collaborators.<br />
<br />
For more information about the project weeks in general, click [[Engineering:Programming_Events|'''here''']]. <br />
<br />
For information about the January 2011 project week, see below.<br />
<br />
For information about Utah as a travel destination click [http://www.utah.com '''here'''].<br />
| style="background: #ebeced" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]<br />
|-<br />
| style="background: #ebeced"|The 2011 AHM, EAB and Project Week will be held <br>'''January 10-14, 2011''', in '''Salt Lake City''', Utah. <br />
|}<br />
<br />
== Dates, Venue, Registration ==<br />
'''Dates:'''<br />
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 13th'''. <br />
* Project Activities will be held rest of the week between '''Monday, January 10th and Friday, January 14th'''.<br />
<br />
'''Venue:''' The venue for the meeting is the Sheraton, Salt Lake City, Utah. Please either call the hotel at +801-401-2000 (toll free) and mention the group code "SCI" or book online [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=1011029581&key=F0B2E '''here''']. Please note that '''''we need attendees to use this hotel''''' in order not to incur additional charges for use of the conference rooms and keep registration fees low. The group rate is $119/night + tax and is valid for reservations made until December 9, 2010. After that it is $199/night + tax.<br />
<br />
'''Registration:''' Please click [http://www.sci.utah.edu/namic2011registration.html '''here'''] to register online before '''January 3, 2011'''. All participants must a pay registration fee ('''$200''' for AHM only, and '''$450''' for AHM+Project Week), which covers our catering and facilities costs.<br />
<br />
'''Meeting Rooms:''' See [http://www.sheratonsaltlakecityhotel.com/floor-plans here] for the floorplan.<br />
<br />
== Agenda== <br />
{| border="1" cellpadding="5"<br />
|- style="background:#eeeeee; color:black" align="left" <br />
| style="width:4%" | '''Time'''<br />
| style="width:12%" | '''Monday, January 10''' <br />
| style="width:12%" | '''Tuesday, January 11'''<br />
| style="width:12%" | '''Wednesday, January 12''' <br />
| style="width:32%" | '''Thursday, January 13 '''<br />
| style="width:12%" | '''Friday, January 14''' <br />
|-<br />
| style="background:#eeeeee; color:black"|<br />
| style="background:#ffffff; color:#522200"| '''[[2011_Winter_Project_Week|Project Activities]] ''' <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons)]<br />
| style="background:#dbf3ff; color:#522200"| '''[[2011_Winter_Project_Week|Project Activities]] ''' <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons)]<br />
| style="background:#dbf3ff; color:#522200"| '''[[2011_Winter_Project_Week|Project Activities]] ''' <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons)]<br />
| style="background:#F2E5D3; color:#522200"| '''AHM, EAB''' <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons, Arches, Deer Valley)]<br />
| style="background:#dbf3ff; color:#522200"|'''[[2011_Winter_Project_Week|Project Activities]] ''' <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons)]<br />
|-<br />
| style="background:#eeeeee; color:black"|'''7:30-8:00''' <br />
| style="background:#ffffff; color:black"| <br />
| style="background:#dbf3ff; color:black"| Breakfast<br />
| style="background:#dbf3ff; color:black"| Breakfast<br />
| style="background:#F2E5D3; color:black"| Breakfast<br />
| style="background:#dbf3ff; color:black"| Breakfast<br />
|-<br />
| style="background:#eeeeee; color:black"|'''8:00-10:00''' <br />
| style="background:#ffffff; color:black"|<br />
| style="background:#dbf3ff; color:black"|8:00-9:00 [[AHM_2011:DBP-Briefing|DBP Briefing]] (Ron Kikinis) <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Deer Valley)]<br>9:30-10:00 [[AHM_2011:2011TrainingCoreVision|Training Core Strategy Session]] <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Deer Valley)]<br>*<br> Project Work <br><br />
| style="background:#dbf3ff; color:black"|Project Work <br> 8-9:30am: [[2011 Winter Project Week:Breakout Multi-Image Engineering|Breakout: Engineering of Multi-Volume Data in Slicer]] <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Arches)]<br><br />
| style="background:#F2E5D3; color:black"|'''8:00''' Introduction, [http://www.spl.harvard.edu/~kikinis Ron Kikinis] <br><br />
'''8:05-10:00 Roadmap Projects'''<br><br />
: 8:05-8:25 Atrial Fibrillation, Rob MacLeod ([[Media:DBP-Afib-1up.pdf|slides (1up)]] and [[Media:DBP-Afib-2up.pdf|slides (2up)]]) <br><br />
: 8:25-8:45 Huntington's Diseases, Hans Johnson ([[Media:20110113_DTI_Intro.pdf|slides]]) <br><br />
: 8:45-9:05 Head and Neck Cancer, Greg Sharp ([[Media:AHM2011-DBP3-HN-Cancer.pdf|slides]])<br><br />
: 9:05-9:25 Traumatic Brain Injury, Jack Van Horn ([[Media:NAMIC-DBP-AHM-2011_pptold.ppt|slides]])<br><br />
: 9:25-9:45 Image Guided Therapy, Nobuhiko Hata ([[Media:AHM2011-IGT-Hata-talk.pptx|slides]]) <br><br />
| style="background:#dbf3ff; color:black"|Project Review <br><br />
|-<br />
| style="background:#eeeeee; color:black"|'''10:00-10:30'''<br />
| style="background:#ffffff; color:black"|<br />
| style="background:#dbf3ff; color:black"| Coffee<br />
| style="background:#dbf3ff; color:black"| Coffee<br />
| style="background:#F2E5D3; color:black"| Coffee<br />
| style="background:#dbf3ff; color:black"| Coffee<br />
|-<br />
| style="background:#eeeeee; color:black"|'''10:30-12:00'''<br />
| style="background:#ffffff; color:black"| '''Vision10'''<br />
| style="background:#dbf3ff; color:black"|[[2011 Winter Project Week:Breakout Slicer|Breakout: Slicer 4 - Looking Forward]] (Steve Pieper, Julien Finet, Jean-Christophe Fillion-Robin)<br>[http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Arches)]<br>*<br> Project Work<br />
| style="background:#dbf3ff; color:black"|[[2011 Winter Project Week:Breakout DTI|Breakout: DTI - Next Generation]] (Hans Johnson, C-F Westin) <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Deer Valley)]<br>*<br> Project Work<br />
<br />
| style="background:#F2E5D3; color:black"|<br />
'''10:30-12:00: Algorithms''' <br><br />
:10:30-10:45 Overview, Ross Whitaker ([[media:NAMIC_AHM_C1_intro_Jan11.ppt|slides]]) <br><br />
:10:45-11:00 Statistical models of anatomy and pathology, Polina Golland ([[media:NAMIC-AHM-2011-StatisticalModels.ppt|slides]]) <br><br />
:11:00-11:15 Geometric correspondence, Guido Gerig ([[media:NAMIC-AHM-Geom-Registration.pdf|pdf slides]]) ([[media:NAMIC-AHM-Geom-Registration.ppt|ppt slides w movies]]) <br><br />
:11:15-11:30 User interactive tools for segmentation, Allen Tannenbaum ([[media:Interactive.segmentation.january.2011.pdf|pdf slides]]) ([[media:Interactive.segmentation.january.2011.pdf|pdf slides]]) <br><br />
:11:30-11:45 Longitudinal and time-series analysis, Martin Styner ([[media:2011_01_NAMIC_LongTimeSeries.pptx|slides]])<br><br />
| style="background:#dbf3ff; color:black"|Project Review<br />
|-<br />
| style="background:#eeeeee; color:black"|'''12:00-1:00''' <br />
| style="background:#dbf3ff; color:black"| Lunch<br />
| style="background:#dbf3ff; color:black"| Lunch <br> <br />
| style="background:#dbf3ff; color:black"| Lunch<br> <br />
| style="background:#F2E5D3; color:black"| Lunch<br />
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br />
|-<br />
| style="background:#eeeeee; color:black"|'''1:00-3:00'''<br />
| style="background:#dbf3ff; color:black"|1:00 '''Welcome''' <br> Ron Kikinis <br> [[2011_Winter_Project_Week:Segment-a-spine|Segment a spine challenge]] <br><br>1:10pm '''Project Introductions''' <br> All Project Leads <br> <br />
| style="background:#dbf3ff; color:black"|1-2pm: [[2011 Winter Project Week:Breakout Pathology and Longitudinal Followup|Breakout: Pathology and Longitudinal Followup]] <br> (Guido Gerig) <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Deer Valley)]<br><br />
2-3pm: [[2011 Winter Project Week:Breakout ShapeWorks|Breakout: Particle Shape Correspondence]] <br> (Martin Styner, Tom Fletcher, Ross Whitaker) <br> (Arches)<br><br />
| style="background:#dbf3ff; color:black"|Project Work <br />
| style="background:#F2E5D3; color:black"|<br />
<br />
'''1:00-2:30 Engineering'''<br><br />
:1:00-1:15 2010 Highlights, Aims, Architecture, Will Schroeder ([[Media:AHM2011-Core1b-Engineering-Architecture.ppt|slides]])<br><br />
:1:15-1:30 End User Platform Slicer 4, Steve Pieper ([[Media:AHM2011-Core1b-Engineering-EndUserPlatform.ppt|slides]])<br><br />
:1:30-1:45 Computational Platform, CLI, Jim Miller ([[Media:AHM2011-Core1b-Engineering-ComputationalPlatform.ppt|slides]])<br><br />
:1:45-2:00 Data Management Platform, Stephen Aylward ([[Media:AHM2011-Core1b-Engineering-DataManagement.ppt|slides]])<br><br />
:2:00-2:15 Software Process, Stephen Aylward ([[Media:AHM2011-Core1b-Engineering-SoftwareProcess.ppt|slides]])<br><br />
'''2:30-3:00 Outreach and Training''' (Sonia Pujol) ([[Media:NA-MIC_TrainingOutreach_AHM2011_SoniaPujol.ppt|slides]]) <br />
| style="background:#ffffff; color:black"|<br />
|-<br />
| style="background:#eeeeee; color:black"|'''3:00-3:30''' <br />
| style="background:#dbf3ff; color:black"| Coffee<br />
| style="background:#dbf3ff; color:black"| Coffee<br />
| style="background:#dbf3ff; color:black"| Coffee<br />
| style="background:#F2E5D3; color:black"| Coffee<br />
| style="background:#ffffff; color:black"|<br />
|-<br />
| style="background:#eeeeee; color:black"|'''3:00-5:00''' <br />
| style="background:#dbf3ff; color:black"|[[2011 Winter Project Week:Breakout Slicer with Ron|Breakout: Slicer with Ron]] (Ron Kikinis)<br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Arches)]<br><br />
| style="background:#dbf3ff; color:black"|4:00-5:00 [[2011 Winter Project Week:BreakoutHD_UNC_Utah|Breakout: DTI analysis & longitudinal analysis for HD]] (Hans Johnson, Guido Gerig, Martin Styner)<br><br />
| style="background:#dbf3ff; color:black"|Project Work <br><br />
| style="background:#F2E5D3; color:black"|[[2011_EAB|EAB]]<br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Deer Valley)] <br> '''3:00-4:00''' Discussion with NA-MIC Leadership<br> '''4:00-5:00''' Closed Session <br />
| style="background:#ffffff; color:black"|<br />
|-<br />
| style="background:#eeeeee; color:black"|'''05:00-07:00''' <br />
| style="background:#dbf3ff; color:black"|<br />
| style="background:#dbf3ff; color:black"|4:30-6:30<br>[[2011_Winter_Project_Week:Breakout_Slicer#Afternoon_Qt_Loadable_Module_Tutorial|How to write a loadable module]](J2, JC)<br />
| style="background:#dbf3ff; color:black"|<br />
| style="background:#F2E5D3; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)<br />
| style="background:#ffffff; color:black"| <br />
|}<br />
<br />
'''General Announcements:'''<br />
<br />
*[[Summer 2011 Tutorial Contest]] Randy Gollub/Sonia Pujol<br />
*[http://www.kitware.com/workshops/SPIE_CAD_2011.html SPIE Demonstration Workshop]<br />
<br />
==Registered Attendees==<br />
<br />
<big>'''NOTE:'''</big> <font color="maroon">The registered attendee list will be posted here by the organizers. '''DO NOT''' add your name to this list yourself.</font> [[User:Tkapur|Tkapur]] 01:19, 5 January 2011 (UTC)<br />
<br />
# Michael Ackerman EAB<br />
# Nicole Aucoin Brigham and Womens Hospital<br />
# Stephen Aylward Kitware<br />
# Dominique Belhachemi University of Pennsylvania<br />
# Josh Blauer, SCI Institute<br />
# Morry Blumenfeld EAB<br />
# Anthony Blumfield Radnostics<br />
# lucile bompard NIRAL<br />
# Francois Budin UNC-NIRAL<br />
# Anna Cariello University of Utah<br />
# Josh Cates SCI Institute<br />
# Micah Chambers UCLA<br />
# Laurent Chauvin Brigham and Womens Hospital<br />
# Min Chen Johns Hopkins University<br />
# Zohara Cohen NIBIB<br />
# Jason Crane UCSF<br />
# Adrian Dalca MIT<br />
# Manasi Datar SCI Institute<br />
# Andriy Fedorov Brigham and Womens Hospital<br />
# Jean-Christophe Fillion-Robin Kitware Inc.<br />
# Julien Finet Kitware Inc.<br />
# Tom Fletcher SCI Institute<br />
# David Fuentes MD Anderson Cancer Center<br />
# Yi Gao Georgia Tech<br />
# Guido Gerig SCI Institute<br />
# Behnood Gholami Georgia Institute of Technology<br />
# Polina Golland MIT<br />
# Randy Gollub Brigham and Womens Hospital<br />
# Alexandre Gouaillard A*STAR<br />
# Daniel Haehn UPenn<br />
# Xiang Hao SCI Institute<br />
# Nobuhiko Hata Brigham and Womens Hospital<br />
# Katie Hayes BWH<br />
# Nicholas Herlambang AZE, Ltd.<br />
# ANDREI IRIMIA University of California, Los Angeles<br />
# Hans Johnson University of Iowa<br />
# Chris Johnson EAB<br />
# Peter Karasev Georgia Tech<br />
# Ron Kikinis Brigham and Womens Hospital<br />
# Ivan Kolesov Georgia Tech<br />
# Janet Lainhart University of Utah<br />
# Andras Lasso School of Computing, Queens University<br />
# Gaetan Lehmann Cosmo Software Inc<br />
# Feng Li Robarts Research Institute<br />
# Yinpeng Li UNC<br />
# Curtis Lisle KnowledgeVis, LLC<br />
# Haiying Liu Covidien<br />
# Bill Lorensen EAB<br />
# Rob MacLeod SCI Institute<br />
# Mahnaz Maddah SRI International <br />
# Vincent Magnotta The University of Iowa<br />
# Daniel Marcus Washington University<br />
# Katie Mastrogiacomo Brigham and Womens Hospital<br />
# Joy Matsui University of Iowa<br />
# Dominik Meier Brigham and Womens Hospital<br />
# bjoern menze CSAIL MIT<br />
# Mikhail Milchenko Washington University in St Louis<br />
# James Miller GE Research<br />
# Karol Miller The University of Western Australia<br />
# Zach Mullen Kitware, Inc<br />
# Sandy Napel EAB<br />
# Vladimir Nikonovskiy Physical Sciences, Inc.<br />
# Lauren ODonnell Brigham and Womens Hospital<br />
# Marram Olson <br />
# Danielle Pace Kitware <br />
# Beatriz Paniagua University of North Carolina at Chapel Hill<br />
# David Partyka Kitware<br />
# Godfrey Pearlson EAB<br />
# Steve Pieper Isomics, Inc.<br />
# Carlo Pierpaoli EAB<br />
# Wendy Plesniak BWH<br />
# Kilian Pohl UPenn<br />
# Marcel Prastawa SCI Institute<br />
# Fred Prior EAB<br />
# Sonia Pujol Brigham Womens Hosp., Harvard University<br />
# Martin Rajchl Robarts Research Institute<br />
# Petter Risholm Brigham and Womens Hospital<br />
# Marco Ruiz UCSD<br />
# Will Schroeder Kitware<br />
# Mark Scully University of Iowa<br />
# Anuja Sharma SCI Institute<br />
# Gregory Sharp MGH<br />
# Dinggang Shen UNC-Chapel Hill<br />
# Liao Shu UNC<br />
# Nadya Shusharina MGH<br />
# Martin Styner University of North Carolina<br />
# Padmavathi Sundaram Children's Hospital Boston<br />
# Suares Tamekue Tatuebu Brigham and Womens Hospital<br />
# Allen Tannenbaum Georgia Tech<br />
# Xiaodong Tao Xiaodong Tao<br />
# Junichi Tokuda Brigham and Womens Hospital<br />
# Tamas Ungi Queens University<br />
#Mustafa Uzunbas Rutgers<br />
# Clement Vachet UNC Chapel Hill<br />
# John Van Horn UCLA<br />
# Gopal Veni SCI Institute<br />
# Bo Wang SCI Institute<br />
# Qian Wang UNC<br />
# Demian Wasserman Harvard Medical School<br />
# Sandy Wells Brigham and Womens Hospital<br />
# Carl-Fredrik Westin Brigham and Womens Hospital<br />
# Ross Whitaker SCI Institute<br />
# Alexander Yarmarkovich ISOMIC<br />
# Terry Yoo National Library of Medicine at NIH<br />
# Alex Zaitzev Brigham and Womens Hospital<br />
# Kris Zygmunt SCI Institute</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Project_Week_DICOM_supplement_145&diff=669882010 Project Week DICOM supplement 1452011-05-04T16:17:01Z<p>Agouaillard: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Mathieu Malaterre: Entrepreneur<br />
* Alex. Gouaillard: A*STAR<br />
* Luis Ibanez: Kitware Inc.<br />
<br />
==Project==<br />
DICOM Supplement 145 provide a way to go over the 32bits limits and allow storing of large images. We propose to implement this specification.<br />
In addition, we would implement DICOM specification for JPEG 2000 Part 2 Multi-component Image Compression. This portion of the standard provides higher<br />
compression ratio for storing multicomponent images. <br />
Finally by implementing DICOM supplement 132, we would provides support for storing of surfaces and 3D volumes, as an addition to the 2D RTSTRUCT.<br />
<br />
<br />
=== Standard support for Large multicomponent images in ITK ===<br />
DICOM currently defines Image IODs by storing the rows and columns as unsigned short<br />
integer. This means that an image can only be at most of size 2^16 * 2^16 pixels.<br />
This is a limitation for Microscopy Images as , for example, typical Whole Slice Images an be 60,000 * 80,000 pixels. Since images are generally stored with 24-bit color<br />
pixels, this means WSI can go up to 15Gb. Confocal Microscopy Images add one additional<br />
dimension, and are today already capable of acquiring 24 channels. They are reported to need up<br />
to petabytes.<br />
For this reason DICOM Supplement 145 defines a way to store images into multiple<br />
DICOM files providing a mean to work around this 32bits limitation of DICOM.<br />
By implementing this Supplement (which is still in Ballot), we would provide to the<br />
ITK community a proof of concept and allow people to start saving larges images using DICOM.<br />
This would allow the re-using of technologies and prevent people from re-inventing the wheel<br />
and start using a new file format to exchange medical image (second system effect). <br />
<br />
<br />
<br />
=== Standard support for multicomponent images compression in ITK ===<br />
Microscopy Images, on top of being larger sometimes by several orders of magnitudes from medical images, are also multi-component. Even though ITK handle multicomponent images per say, by defining the right pixel type, nothing is available today for the storage and compression of images that would have more than 3 channels (RGB). Since 2001, the DICOM standard allows JPEG 2000 compression. GDCM 2.x has supported a portion of the standard by providing an API to allow transfer syntax such as JPEG 2000 Image Compression (1.2.840.10008.1.2.4.90 and 1.2.840.10008.1.2.4.91). However the standard also includes JPEG 2000 Part 2 Multi-component Image Compression (1.2.840.10008.1.2.4.92 and 1.2.840.10008.1.2.4.93). The latter has never made into GDCM / ITK, or any other open source DICOM toolkit, since as quoted from the presentation: “Image Compression Refresher – JPEG 2000 and 3D, David Clunie”: the compression gain was modest (using lossless compression). We see now an opportunity that this compression can make it into GDCM / ITK since microscopy images would perfectly fit into the original design of the compression (ISO/IEC 15444-2:2003 Annex J). This would ease the dissemination of large dataset by reusing standard compression techniques, since this would greatly reduce the size of those file datasets. This will be particularly useful for microscopic images. At the time of writing no other open-source DICOM toolkit offer this compression algorithm. <br />
<br />
<br />
<br />
=== Standard support for discrete 2 and 3 manifold storage in ITK ===<br />
From its early design, ITK has always offered some n-dimensional n-manifold (polygonal meshes) support through the itk::Mesh class. However at the time of writing of this proposal, there is still no official way to read or write those meshes from and to a filesystem in ITK. Only an hybrid solution is available in Insight Applications. However it implies a dependency to the entire VTK library which is an overkill most of the time.<br />
Thanks to the work on itk::QuadEdgeMesh some progress have been made toward that goal. The Review directory surrently holds a very simple VTK PolyData reader and writer. However, it only supports legacy vtk files using ASCII encoding. For its defense, this implementation was only made for regression testing and illustration of the filters usage.<br />
We are proposing here to fill this gap in the ITK toolkit and implement DICOM's Supplement 132, part of the standard since 2008, which would add surfaces and volumes meshes (2 and 3 manifolds) storage capacity to GDCM /ITK. This would add support for surfaces and volume (2 and 3 manifolds in n dimensional space, see supplemental material annex).<br />
We suggest 2 different options. The first option would allow for storage of itk::QuadEdgeMesh as a DICOM file. The second options would allow for storage of an itk::Mesh as a DICOM file. Of course reading the corresponding structures from a DICOM file would also be provided.<br />
As an illustration, we make a clear distinction in what itk::QuadEdgeMesh handles and what itk::Mesh can handle. Both 2 and 3 manifold objects are handled in the DICOM standard.<br />
We do anticipate a large portion of this task to be validation testing. Since there are no other serialization mechanism available in ITK, we will need to setup an hybrid system with VTK to perform validation on the dataset written (a 3D VTK mesh will be used as input for the tests). For this we would be re-using code from InsightApplications/Auxiliary/vtk/vtk2itk.cxx.<br />
<br />
<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
The objectives of the project week is to share with the community and make a list of persons interested and of corresponding efforts before we start implementing. Typically at the end of the week we would like to have identified existing parts, ongoing effort and have a roadmap available possibly with other groups joining in depending on needs, manpower and expertise.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
'''1.''' Item #1: Compare existing technologies: HDF5, DICOM, JPEG2000, TIFF (XMP)<br />
<br />
'''2.''' Item #2: Identify technologies in ITK: openjpeg v1 which does not support tiles (required for streaming)<br />
<br />
'''3.''' Item #3: Identify group which would need this technology: maybe CTK ?<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
'''*''' Worked with Kishore for ITK/JPEG 2000 reader. Code review / Made it compile<br />
<br />
'''*''' Sync with upstream openjpeg team: there are 400 regression tests now !<br />
<br />
'''*''' Need to synchronize effort with GDCM 2.x and OpenJPEG v2 update. Prepare patch for GDCM 2.x to use openjpeg v2.<br />
<br />
'''*''' Worked with GoFigure2 team to identify the need:<br />
** passing algorithm more than passing data.<br />
** image data<br />
** very large image 4D<br />
** mesh based segmentation (2d / 3d mesh)<br />
** annotations (label)<br />
<br />
'''*''' XMP technogoly is based on XML, which imply ASCII serialization (poor performance, very verbose).<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a<br />
<br />
* ITK Module<br />
* Other: GDCM extension (gdcm is included in ITK)<br />
<br />
==References==<br />
*the official DICOM Standard Proposal [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf here]<br />
<br />
</div></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Project_Week_DICOM_supplement_145&diff=669872010 Project Week DICOM supplement 1452011-05-04T16:15:20Z<p>Agouaillard: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Mathieu Malaterre: CoSMo Software<br />
* Alex. Gouaillard: A*STAR<br />
* Luis Ibanez: Kitware Inc.<br />
<br />
==Project==<br />
DICOM Supplement 145 provide a way to go over the 32bits limits and allow storing of large images. We propose to implement this specification.<br />
In addition, we would implement DICOM specification for JPEG 2000 Part 2 Multi-component Image Compression. This portion of the standard provides higher<br />
compression ratio for storing multicomponent images. <br />
Finally by implementing DICOM supplement 132, we would provides support for storing of surfaces and 3D volumes, as an addition to the 2D RTSTRUCT.<br />
<br />
<br />
=== Standard support for Large multicomponent images in ITK ===<br />
DICOM currently defines Image IODs by storing the rows and columns as unsigned short<br />
integer. This means that an image can only be at most of size 2^16 * 2^16 pixels.<br />
This is a limitation for Microscopy Images as , for example, typical Whole Slice Images an be 60,000 * 80,000 pixels. Since images are generally stored with 24-bit color<br />
pixels, this means WSI can go up to 15Gb. Confocal Microscopy Images add one additional<br />
dimension, and are today already capable of acquiring 24 channels. They are reported to need up<br />
to petabytes.<br />
For this reason DICOM Supplement 145 defines a way to store images into multiple<br />
DICOM files providing a mean to work around this 32bits limitation of DICOM.<br />
By implementing this Supplement (which is still in Ballot), we would provide to the<br />
ITK community a proof of concept and allow people to start saving larges images using DICOM.<br />
This would allow the re-using of technologies and prevent people from re-inventing the wheel<br />
and start using a new file format to exchange medical image (second system effect). <br />
<br />
<br />
<br />
=== Standard support for multicomponent images compression in ITK ===<br />
Microscopy Images, on top of being larger sometimes by several orders of magnitudes from medical images, are also multi-component. Even though ITK handle multicomponent images per say, by defining the right pixel type, nothing is available today for the storage and compression of images that would have more than 3 channels (RGB). Since 2001, the DICOM standard allows JPEG 2000 compression. GDCM 2.x has supported a portion of the standard by providing an API to allow transfer syntax such as JPEG 2000 Image Compression (1.2.840.10008.1.2.4.90 and 1.2.840.10008.1.2.4.91). However the standard also includes JPEG 2000 Part 2 Multi-component Image Compression (1.2.840.10008.1.2.4.92 and 1.2.840.10008.1.2.4.93). The latter has never made into GDCM / ITK, or any other open source DICOM toolkit, since as quoted from the presentation: “Image Compression Refresher – JPEG 2000 and 3D, David Clunie”: the compression gain was modest (using lossless compression). We see now an opportunity that this compression can make it into GDCM / ITK since microscopy images would perfectly fit into the original design of the compression (ISO/IEC 15444-2:2003 Annex J). This would ease the dissemination of large dataset by reusing standard compression techniques, since this would greatly reduce the size of those file datasets. This will be particularly useful for microscopic images. At the time of writing no other open-source DICOM toolkit offer this compression algorithm. <br />
<br />
<br />
<br />
=== Standard support for discrete 2 and 3 manifold storage in ITK ===<br />
From its early design, ITK has always offered some n-dimensional n-manifold (polygonal meshes) support through the itk::Mesh class. However at the time of writing of this proposal, there is still no official way to read or write those meshes from and to a filesystem in ITK. Only an hybrid solution is available in Insight Applications. However it implies a dependency to the entire VTK library which is an overkill most of the time.<br />
Thanks to the work on itk::QuadEdgeMesh some progress have been made toward that goal. The Review directory surrently holds a very simple VTK PolyData reader and writer. However, it only supports legacy vtk files using ASCII encoding. For its defense, this implementation was only made for regression testing and illustration of the filters usage.<br />
We are proposing here to fill this gap in the ITK toolkit and implement DICOM's Supplement 132, part of the standard since 2008, which would add surfaces and volumes meshes (2 and 3 manifolds) storage capacity to GDCM /ITK. This would add support for surfaces and volume (2 and 3 manifolds in n dimensional space, see supplemental material annex).<br />
We suggest 2 different options. The first option would allow for storage of itk::QuadEdgeMesh as a DICOM file. The second options would allow for storage of an itk::Mesh as a DICOM file. Of course reading the corresponding structures from a DICOM file would also be provided.<br />
As an illustration, we make a clear distinction in what itk::QuadEdgeMesh handles and what itk::Mesh can handle. Both 2 and 3 manifold objects are handled in the DICOM standard.<br />
We do anticipate a large portion of this task to be validation testing. Since there are no other serialization mechanism available in ITK, we will need to setup an hybrid system with VTK to perform validation on the dataset written (a 3D VTK mesh will be used as input for the tests). For this we would be re-using code from InsightApplications/Auxiliary/vtk/vtk2itk.cxx.<br />
<br />
<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
The objectives of the project week is to share with the community and make a list of persons interested and of corresponding efforts before we start implementing. Typically at the end of the week we would like to have identified existing parts, ongoing effort and have a roadmap available possibly with other groups joining in depending on needs, manpower and expertise.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
'''1.''' Item #1: Compare existing technologies: HDF5, DICOM, JPEG2000, TIFF (XMP)<br />
<br />
'''2.''' Item #2: Identify technologies in ITK: openjpeg v1 which does not support tiles (required for streaming)<br />
<br />
'''3.''' Item #3: Identify group which would need this technology: maybe CTK ?<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
'''*''' Worked with Kishore for ITK/JPEG 2000 reader. Code review / Made it compile<br />
<br />
'''*''' Sync with upstream openjpeg team: there are 400 regression tests now !<br />
<br />
'''*''' Need to synchronize effort with GDCM 2.x and OpenJPEG v2 update. Prepare patch for GDCM 2.x to use openjpeg v2.<br />
<br />
'''*''' Worked with GoFigure2 team to identify the need:<br />
** passing algorithm more than passing data.<br />
** image data<br />
** very large image 4D<br />
** mesh based segmentation (2d / 3d mesh)<br />
** annotations (label)<br />
<br />
'''*''' XMP technogoly is based on XML, which imply ASCII serialization (poor performance, very verbose).<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a<br />
<br />
* ITK Module<br />
* Other: GDCM extension (gdcm is included in ITK)<br />
<br />
==References==<br />
*the official DICOM Standard Proposal [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf here]<br />
<br />
</div></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=Paraview_Support_for_Computational_Anatomy&diff=55425Paraview Support for Computational Anatomy2010-06-25T14:43:15Z<p>Agouaillard: /* Delivery Mechanism */</p>
<hr />
<div>__NOTOC__<br />
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''<br />
<gallery><br />
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.<br />
Image:ParaviewScene.png|Scene instantiated under Paraview.<br />
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.<br />
</gallery><br />
==Key Investigators==<br />
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder<br />
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller<br />
* CoSMo: Alex. Gouaillard<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy. <br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc. <br />
* Interaction possible between Slicer and Paraview. <br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes. <br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.<br />
<br />
Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter (http://www.cis.jhu.edu/software/laplace-beltrami/) into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouaillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop. <br />
<br />
Thanks to Curtis Lisle for converting the film to Quicktime mov format. <br />
<br />
[[Media:LeftAmygdalaSurfaceHarmonics.mov| Click here for a quicktime video]]<br />
<br />
==References==<br />
* http://www.paraview.org/<br />
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)<br />
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694. <br />
</div></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=Paraview_Support_for_Computational_Anatomy&diff=55424Paraview Support for Computational Anatomy2010-06-25T14:42:16Z<p>Agouaillard: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''<br />
<gallery><br />
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.<br />
Image:ParaviewScene.png|Scene instantiated under Paraview.<br />
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.<br />
</gallery><br />
==Key Investigators==<br />
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder<br />
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller<br />
* CoSMo: Alex. Gouaillard<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy. <br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc. <br />
* Interaction possible between Slicer and Paraview. <br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes. <br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.<br />
<br />
Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter (http://www.cis.jhu.edu/software/laplace-beltrami/) into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop. <br />
<br />
Thanks to Curtis Lisle for converting the film to Quicktime mov format. <br />
<br />
[[Media:LeftAmygdalaSurfaceHarmonics.mov| Click here for a quicktime video]]<br />
<br />
==References==<br />
* http://www.paraview.org/<br />
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)<br />
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694. <br />
</div></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week_Microscopy_extensions_for_ITK&diff=554232010 Summer Project Week Microscopy extensions for ITK2010-06-25T14:41:20Z<p>Agouaillard: /* Usability */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Back to Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Gaetan lehmann: INRA<br />
* Alex Gouaillard: CoSMo Software / A*STAR<br />
* Luis Ibanez: Kitware Inc.<br />
<br />
== Introduction ==<br />
Fluorescence microscopy is a very common image acquisition modality, used in many fields including medical imaging and biological research. Depending on the techniques used, the images produced can be in 2D or 3D, time lapse, and contain several channels.<br />
ITK provides a lot of useful tools to analyze the images produce in fluorescence microscopy. The N-dimensionality of ITK is especially useful when dealing with 3D data sets. However, it contains very few methods to correct the aberrations introduced in the image during the acquisition.<br />
We propose to implement some tools dedicated to the restoration of images in fluorescence microscopy. Because no algorithm exists to perfectly correct those aberrations, we propose to implement several algorithms for each kind of problem, including the most common algorithms, which are well know and widely used, and some of the state of the art algorithms.<br />
<br />
Bold and Tag'ed with a #, working prototype available.<br />
<br />
Bold and tag'ed with a @, prototype expected on or before august<br />
<br />
=== preliminary work ===<br />
* '''fft convolution #''' ( [http://hdl.handle.net/10380/3154 Insight Journal publication] )<br />
Most of the deconvolution methods are based on multiple deconvolution or on FFT transforms. This preliminary work will be very useful to implement the deconvolution filters.<br />
* '''noise simulation #''' ( [http://hdl.handle.net/10380/3158 Insight Journal publication] )<br />
Being able to simulate the noise behavior is very important because it let the user compare the result of a restoration method with the known unblurred object.<br />
<br />
=== Deconvolution ===<br />
* non-blind deconvolution<br />
This is the most common deconvolution type. With all those methods, it is supposed that the point spread function is known. Most of those methods, for practical reasons, also assume that the point spread function (PSF) is spatially invariant in the image. Some of the methods are focused on the computation efficiency, at the cost of the restoration quality - often the linear algorithms -, and some on the restoration quality at the cost of the computation complexity - usually the iterative algorithms. The fluorescence noise follows a Poisson distribution, but is often considered as gaussian noise to simplify the computations. This assumption is generally valid when the SNR is high - most of the time for wide field microscopy. Because of the noise amplification produce by the deconvolution process, most of the methods are regularized. In fact, the only unregularized methods are iterative, and are effectively regularized by stopping the iteration process before the convergence.<br />
<br />
* Space invariant PSF - Linear algorithms<br />
All the proposed linear algorithms are made with the assumption of an additive gaussian noise. Other algorithms combined with wavelet transformed produce better results. <br />
<br />
# '''Regularized Linear Least Squares (truncated SVD) #'''<br />
# '''Maximum A Posteriori Linear Least Squares #'''<br />
# '''Wiener #'''<br />
# '''Tikhonov Miller #'''<br />
<br />
* Space Invariant - Iterative Algorithms<br />
# '''van Cittert #''': No noise assumption. A single convolution is required by iteration.<br />
# '''Jansson-van Cittert #''': This is a constrained version of the van Cittert algorithm. The pixel values are constrained in a range of values.<br />
# '''Landweber #''': The noise is assumed to follow a gaussian additive model. The algorithm requires two convolutions by iteration and the step size is fixed, which makes it converge slowly. It can be optionally constrained to avoid negative values as expected in fluorescence microscopy.<br />
# '''Richardson-Lucy #''': The noise is assumed to follow a poisson model. The algorithm requires two convolutions by iteration and the step size is fixed, which makes it converge slowly. The non negativity property is ensured without additional constraint. This algorithm is also known as Maximum Likelihood Maximization Expectation.<br />
# '''Damped Richardson-Lucy #''' This is a simple regularized version of the Richardson-Lucy algorithm. It is widely used in astronomy.<br />
# '''Tikhonov-Miller regularized Richardson-Lucy #''': This is a regularized version of the Richardson-Lucy algorithm using the Tikhonov-Miller usual penalization. Ref: Dey et al. 3D Microscopy Deconvolution using Richardson-Lucy Algorithm with Total Variation Regularization. hal.archives-ouvertes.fr (2004)<br />
# Total variation regularized Richardson-Lucy: This is a regularized version of the Richardson-Lucy algorithm which also minimize the Total Variation of the image to avoid the noise amplification.<br />
# '''Maximum Entropy regularized Richardson-Lucy #''': This is a regularized version of the Richardson lucy algoritm by imposing a maximum entropy constraint on the unblurred image.<br />
# Good regularized Richardson-Lucy: This is a regularize Richardson-Lucy algorithm which also minimize the Good's roughness.<br />
# '''Iterative Constrained Tikhonov-Miller @''': The noise is assumed to follow an additive gaussian model, and the process is regularized using the usual penalization. The non negativity is enforced at each iteration and the convergence is accelerated with a conjugate gradient acceleration. <br />
# Verveer's Maximum A Posteriori (MAPGG, MAPGE, MAPPG, MAPPE, MAPGR and MAPPR): The noise is assumed to follow either a gaussian or a poisson model. Three different a priori can be imposed on the unblurred image: a gaussian model, a maximum entroy or a Good's roughness. The process is accelerated with a Newton acceleration.<br />
# Markov Random Field MAP: The noise is assumed to follow a poisson model. The unblurred image is assumed to be a realization of a Markov random field. The problem is solved with a split gradient technique which is known to converge slowly, but the result quality is enhance compared to other state of the art algorithms.<br />
# Generalized Vector-Valued Total Variation: The noise is assumed to follow an additive gaussian model. The process also minimize the total variation and is accelerated. The code is available for matlab with a BSD license.<br />
* space variant psf<br />
# Depth-variant ML-EM<br />
* PSF<br />
The PSF is required for all the non-blind deconvolution methods. It is possible to get it either by measuring it with beads, are with a model. One way are the other both have their advantages and inconvenience and should be available for the final user.<br />
# PSF simulation<br />
# measurement / Evaluation of psf<br />
* Regularization Parameters Estimation<br />
# Generalized Cross Validation (GCV): A good estimation can be computed for the Tikhonov-Miller regularization with the generalized cross validation method.<br />
<br />
=== Usability ===<br />
On the implementation side, several goal should be reached.<br />
# '''observability #''': The iterative deconvolution algorithm are usually quite long to run - several minutes or tens of minutes on todays computers. As a consequence, it is important that the process can be observed by the user so that he can validate visually the intermediate results. The various measurements made should also be available during the process. If the result is not the expected one, or if the expected result is reach sooner than expected, the user should be able to interrupt the process cleanly.<br />
# '''continue a completed process to increase the number of iterations #''': The iterative filter should provide a mechanism to restart a completed deconvolution in order to increase the number of iterations.<br />
# '''preconditionning #''': Preconditionning is a usual technique where the blurred image and/or the PSF are transformed at the beginning at the deconvolution in order to improve the deconvolution quality or to decrease the number of iterations needed to reach the convergence. The usual precoditionning methods include the gaussian blurring, the Wiener fieltering and various denoising methods (mostly wavelet based).<br />
# multithreaded calculators: ITK does not currently provide any base class to easily implement multithreading in the calculators. We propose to implement such a base class and to use it in the calculators required in the other tasks.<br />
# '''FFTW wisdom integration #''': FFTW provides a mechanism to store the optimized plans on the disk. We propose to use this capability in ITK FFTW filters and to make it's usage transparent for the user.<br />
<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
The objectives of the project week is to share with the community the filters to come to avoid multiple groups working on the same algorithms. Persons interested can contact gaetan or alex directly. <br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
Transition as many filters as possible to the Insight Journal.<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Update the denoising and FFT aricles in IJ<br />
* prepare the tests and papers for the blind deconvolution algorithms<br />
* discuss with another team funded for deconvolution through A2D2<br />
* attend the microscopy workshop and synchronized effort<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
This work will be (eventually) delivered to the NA-MIC Kit as an<br />
#ITK Module<br />
<br />
<br />
==References==<br />
[01] Ref: Preza et al. Regularized method for reconstruction of three-dimensional microscopic objects from optical sections. Journal of the Optical Society of America (1992) vol. 9 (2) pp. 219-228<br><br />
[02] Ref: Preza et al. Image reconstruction for 3-D light microscopy with a regularized linear method incorporating a smoothness prior. Presented at the IS&T/SPIE Symposium on Electronic Imaging (1993) vol. 1905 (129-139)<br><br />
[03] Ref: Richardson. Bayesian-Based Iterative Method of Image Restoration. Journal of the Optical Society of America (1917-1983) (1972) vol. 62 pp. 55-+<br><br />
[04] Ref: Lucy. An iterative technique for the rectification of observed distributions. Astronomical Journal (1974) vol. 79 pp. 745-+<br><br />
[05] Ref: White. Image Restoration Using the Damped Richardson-Lucy Iteration. Proceedings (1994) vol. 61 pp. 292-+<br><br />
[06] Ref: Dey et al. 3D Microscopy Deconvolution using Richardson-Lucy Algorithm with Total Variation Regularization. hal.archives-ouvertes.fr (2004)<br><br />
[07] Ref: Monvel et al. Image Restoration for Confocal Microscopy: Improving the Limits of Deconvolution, with Application to the Visualization of the Mammalian Hearing Organ. Biophysical Journal (2001)<br><br />
[08] Ref: Verveer et Jovin. Acceleration of the ICTM image restoration algorithm. Journal of Microscopy (1997) (188) pp. 191–195<br><br />
[09] Ref: Verveer. Computational and Optical Methods for Improving Resolution and Signal Quality in Fluorescence Microscopy. adsabs.harvard.edu (1998)<br><br />
[10] Ref: Vicidomini et al. Application of the split-gradient method to 3D image deconvolution in fluorescence microscopy. Journal of Microscopy (2009) vol. 234 (1) pp. 47-61<br><br />
[11] Ref: P. Rodriguez, B. Wohlberg, "Efficient Minimization Method for a Generalized Total Variation Functional" IEEE Transactions on Image Processing, 2009, 18:2(322-332)<br><br />
[12] Ref: Preza et Conchello. Depth-variant maximum-likelihood restoration for three-dimensional fluorescence microscopy. Journal of the Optical Society of America A (2004) vol. 21 (9) pp. 1593-1601<br><br />
[13] Ref: Agard. Optical sectioning microscopy: cellular architecture in three dimensions. Annual review of Biophysics and Bioengineering (1984) vol. 13 pp. 191-219<br><br />
[14] Ref: Gibson et Lanni. Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy. J. Opt. Soc. Am. A (1992) vol. 9 (1) pp. 154-166<br><br />
[15] Ref: Haeberle. Focusing of light through a stratified medium: a practical approach for computing microscope point spread functions. Part I: Conventional microscopy. Optics Communications (2003) vol. 216 (1-3) pp. 55 - 63<br><br />
[16] Ref: Haeberle. Focusing of light through a stratified medium: a practical approach for computing microscope point spread functions: Part II: confocal and multiphoton microscopy. Optics Communications (2004) vol. 235 (1-3) pp. 1 - 10<br><br />
[17] Ref: Dey et al. 3D Microscopy Deconvolution using Richardson-Lucy Algorithm with Total Variation Regularization. hal.archives-ouvertes.fr (2004)<br><br />
[18] Ref: Van Kempen et al. A quantitative comparison of image restoration methods for confocal microscopy. Journal of Microscopy (1997) vol. 185 (3) pp. 354-365<br><br />
<br />
</div></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week_Microscopy_extensions_for_ITK&diff=554222010 Summer Project Week Microscopy extensions for ITK2010-06-25T14:41:01Z<p>Agouaillard: /* Usability */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Back to Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Gaetan lehmann: INRA<br />
* Alex Gouaillard: CoSMo Software / A*STAR<br />
* Luis Ibanez: Kitware Inc.<br />
<br />
== Introduction ==<br />
Fluorescence microscopy is a very common image acquisition modality, used in many fields including medical imaging and biological research. Depending on the techniques used, the images produced can be in 2D or 3D, time lapse, and contain several channels.<br />
ITK provides a lot of useful tools to analyze the images produce in fluorescence microscopy. The N-dimensionality of ITK is especially useful when dealing with 3D data sets. However, it contains very few methods to correct the aberrations introduced in the image during the acquisition.<br />
We propose to implement some tools dedicated to the restoration of images in fluorescence microscopy. Because no algorithm exists to perfectly correct those aberrations, we propose to implement several algorithms for each kind of problem, including the most common algorithms, which are well know and widely used, and some of the state of the art algorithms.<br />
<br />
Bold and Tag'ed with a #, working prototype available.<br />
<br />
Bold and tag'ed with a @, prototype expected on or before august<br />
<br />
=== preliminary work ===<br />
* '''fft convolution #''' ( [http://hdl.handle.net/10380/3154 Insight Journal publication] )<br />
Most of the deconvolution methods are based on multiple deconvolution or on FFT transforms. This preliminary work will be very useful to implement the deconvolution filters.<br />
* '''noise simulation #''' ( [http://hdl.handle.net/10380/3158 Insight Journal publication] )<br />
Being able to simulate the noise behavior is very important because it let the user compare the result of a restoration method with the known unblurred object.<br />
<br />
=== Deconvolution ===<br />
* non-blind deconvolution<br />
This is the most common deconvolution type. With all those methods, it is supposed that the point spread function is known. Most of those methods, for practical reasons, also assume that the point spread function (PSF) is spatially invariant in the image. Some of the methods are focused on the computation efficiency, at the cost of the restoration quality - often the linear algorithms -, and some on the restoration quality at the cost of the computation complexity - usually the iterative algorithms. The fluorescence noise follows a Poisson distribution, but is often considered as gaussian noise to simplify the computations. This assumption is generally valid when the SNR is high - most of the time for wide field microscopy. Because of the noise amplification produce by the deconvolution process, most of the methods are regularized. In fact, the only unregularized methods are iterative, and are effectively regularized by stopping the iteration process before the convergence.<br />
<br />
* Space invariant PSF - Linear algorithms<br />
All the proposed linear algorithms are made with the assumption of an additive gaussian noise. Other algorithms combined with wavelet transformed produce better results. <br />
<br />
# '''Regularized Linear Least Squares (truncated SVD) #'''<br />
# '''Maximum A Posteriori Linear Least Squares #'''<br />
# '''Wiener #'''<br />
# '''Tikhonov Miller #'''<br />
<br />
* Space Invariant - Iterative Algorithms<br />
# '''van Cittert #''': No noise assumption. A single convolution is required by iteration.<br />
# '''Jansson-van Cittert #''': This is a constrained version of the van Cittert algorithm. The pixel values are constrained in a range of values.<br />
# '''Landweber #''': The noise is assumed to follow a gaussian additive model. The algorithm requires two convolutions by iteration and the step size is fixed, which makes it converge slowly. It can be optionally constrained to avoid negative values as expected in fluorescence microscopy.<br />
# '''Richardson-Lucy #''': The noise is assumed to follow a poisson model. The algorithm requires two convolutions by iteration and the step size is fixed, which makes it converge slowly. The non negativity property is ensured without additional constraint. This algorithm is also known as Maximum Likelihood Maximization Expectation.<br />
# '''Damped Richardson-Lucy #''' This is a simple regularized version of the Richardson-Lucy algorithm. It is widely used in astronomy.<br />
# '''Tikhonov-Miller regularized Richardson-Lucy #''': This is a regularized version of the Richardson-Lucy algorithm using the Tikhonov-Miller usual penalization. Ref: Dey et al. 3D Microscopy Deconvolution using Richardson-Lucy Algorithm with Total Variation Regularization. hal.archives-ouvertes.fr (2004)<br />
# Total variation regularized Richardson-Lucy: This is a regularized version of the Richardson-Lucy algorithm which also minimize the Total Variation of the image to avoid the noise amplification.<br />
# '''Maximum Entropy regularized Richardson-Lucy #''': This is a regularized version of the Richardson lucy algoritm by imposing a maximum entropy constraint on the unblurred image.<br />
# Good regularized Richardson-Lucy: This is a regularize Richardson-Lucy algorithm which also minimize the Good's roughness.<br />
# '''Iterative Constrained Tikhonov-Miller @''': The noise is assumed to follow an additive gaussian model, and the process is regularized using the usual penalization. The non negativity is enforced at each iteration and the convergence is accelerated with a conjugate gradient acceleration. <br />
# Verveer's Maximum A Posteriori (MAPGG, MAPGE, MAPPG, MAPPE, MAPGR and MAPPR): The noise is assumed to follow either a gaussian or a poisson model. Three different a priori can be imposed on the unblurred image: a gaussian model, a maximum entroy or a Good's roughness. The process is accelerated with a Newton acceleration.<br />
# Markov Random Field MAP: The noise is assumed to follow a poisson model. The unblurred image is assumed to be a realization of a Markov random field. The problem is solved with a split gradient technique which is known to converge slowly, but the result quality is enhance compared to other state of the art algorithms.<br />
# Generalized Vector-Valued Total Variation: The noise is assumed to follow an additive gaussian model. The process also minimize the total variation and is accelerated. The code is available for matlab with a BSD license.<br />
* space variant psf<br />
# Depth-variant ML-EM<br />
* PSF<br />
The PSF is required for all the non-blind deconvolution methods. It is possible to get it either by measuring it with beads, are with a model. One way are the other both have their advantages and inconvenience and should be available for the final user.<br />
# PSF simulation<br />
# measurement / Evaluation of psf<br />
* Regularization Parameters Estimation<br />
# Generalized Cross Validation (GCV): A good estimation can be computed for the Tikhonov-Miller regularization with the generalized cross validation method.<br />
<br />
=== Usability ===<br />
On the implementation side, several goal should be reached.<br />
# '''observability #''': The iterative deconvolution algorithm are usually quite long to run - several minutes or tens of minutes on todays computers. As a consequence, it is important that the process can be observed by the user so that he can validate visually the intermediate results. The various measurements made should also be available during the process. If the result is not the expected one, or if the expected result is reach sooner than expected, the user should be able to interrupt the process cleanly.<br />
# '''continue a completed process to increase the number of iterations #''': The iterative filter should provide a mechanism to restart a completed deconvolution in order to increase the number of iterations.<br />
# '''preconditionning #''': Preconditionning is a usual technique where the blurred image and/or the PSF are transformed at the beginning at the deconvolution in order to improve the deconvolution quality or to decrease the number of iterations needed to reach the convergence. The usual precoditionning methods include the gaussian blurring, the Wiener fieltering and various denoising methods (mostly wavelet based).<br />
# multithreaded calculators: ITK does not currently provide any base class to easily implement multithreading in the calculators. We propose to implement such a base class and to use it in the calculators required in the other tasks.<br />
# '''FFTW wisdom integration #''': FFTW provides a mechanism to store the optimized plans on the disk. We propose to use this capability in ITK FFTW filters and to make it's usage transparent for the user.<br />
<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
The objectives of the project week is to share with the community the filters to come to avoid multiple groups working on the same algorithms. Persons interested can contact gaetan or alex directly. <br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
Transition as many filters as possible to the Insight Journal.<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
- Update the denoising and FFT aricles in IJ<br />
- prepare the tests and papers for the blind deconvolution algorithms<br />
- discuss with another team funded for deconvolution through A2D2<br />
- attend the microscopy workshop and synchronized effort<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
This work will be (eventually) delivered to the NA-MIC Kit as an<br />
#ITK Module<br />
<br />
<br />
==References==<br />
[01] Ref: Preza et al. Regularized method for reconstruction of three-dimensional microscopic objects from optical sections. Journal of the Optical Society of America (1992) vol. 9 (2) pp. 219-228<br><br />
[02] Ref: Preza et al. Image reconstruction for 3-D light microscopy with a regularized linear method incorporating a smoothness prior. Presented at the IS&T/SPIE Symposium on Electronic Imaging (1993) vol. 1905 (129-139)<br><br />
[03] Ref: Richardson. Bayesian-Based Iterative Method of Image Restoration. Journal of the Optical Society of America (1917-1983) (1972) vol. 62 pp. 55-+<br><br />
[04] Ref: Lucy. An iterative technique for the rectification of observed distributions. Astronomical Journal (1974) vol. 79 pp. 745-+<br><br />
[05] Ref: White. Image Restoration Using the Damped Richardson-Lucy Iteration. Proceedings (1994) vol. 61 pp. 292-+<br><br />
[06] Ref: Dey et al. 3D Microscopy Deconvolution using Richardson-Lucy Algorithm with Total Variation Regularization. hal.archives-ouvertes.fr (2004)<br><br />
[07] Ref: Monvel et al. Image Restoration for Confocal Microscopy: Improving the Limits of Deconvolution, with Application to the Visualization of the Mammalian Hearing Organ. Biophysical Journal (2001)<br><br />
[08] Ref: Verveer et Jovin. Acceleration of the ICTM image restoration algorithm. Journal of Microscopy (1997) (188) pp. 191–195<br><br />
[09] Ref: Verveer. Computational and Optical Methods for Improving Resolution and Signal Quality in Fluorescence Microscopy. adsabs.harvard.edu (1998)<br><br />
[10] Ref: Vicidomini et al. Application of the split-gradient method to 3D image deconvolution in fluorescence microscopy. Journal of Microscopy (2009) vol. 234 (1) pp. 47-61<br><br />
[11] Ref: P. Rodriguez, B. Wohlberg, "Efficient Minimization Method for a Generalized Total Variation Functional" IEEE Transactions on Image Processing, 2009, 18:2(322-332)<br><br />
[12] Ref: Preza et Conchello. Depth-variant maximum-likelihood restoration for three-dimensional fluorescence microscopy. Journal of the Optical Society of America A (2004) vol. 21 (9) pp. 1593-1601<br><br />
[13] Ref: Agard. Optical sectioning microscopy: cellular architecture in three dimensions. Annual review of Biophysics and Bioengineering (1984) vol. 13 pp. 191-219<br><br />
[14] Ref: Gibson et Lanni. Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy. J. Opt. Soc. Am. A (1992) vol. 9 (1) pp. 154-166<br><br />
[15] Ref: Haeberle. Focusing of light through a stratified medium: a practical approach for computing microscope point spread functions. Part I: Conventional microscopy. Optics Communications (2003) vol. 216 (1-3) pp. 55 - 63<br><br />
[16] Ref: Haeberle. Focusing of light through a stratified medium: a practical approach for computing microscope point spread functions: Part II: confocal and multiphoton microscopy. Optics Communications (2004) vol. 235 (1-3) pp. 1 - 10<br><br />
[17] Ref: Dey et al. 3D Microscopy Deconvolution using Richardson-Lucy Algorithm with Total Variation Regularization. hal.archives-ouvertes.fr (2004)<br><br />
[18] Ref: Van Kempen et al. A quantitative comparison of image restoration methods for confocal microscopy. Journal of Microscopy (1997) vol. 185 (3) pp. 354-365<br><br />
<br />
</div></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week_Microscopy_extensions_for_ITK&diff=537942010 Summer Project Week Microscopy extensions for ITK2010-06-14T05:40:59Z<p>Agouaillard: /* Usability */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Back to Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Gaetan lehmann: INRA<br />
* Alex Gouaillard: CoSMo Software / A*STAR<br />
* NAMIC: (luis?)<br />
<br />
<br />
== Introduction ==<br />
Fluorescence microscopy is a very common image acquisition modality, used in many fields including medical imaging and biological research. Depending on the techniques used, the images produced can be in 2D or 3D, time lapse, and contain several channels.<br />
ITK provides a lot of useful tools to analyze the images produce in fluorescence microscopy. The N-dimensionality of ITK is especially useful when dealing with 3D data sets. However, it contains very few methods to correct the aberrations introduced in the image during the acquisition.<br />
We propose to implement some tools dedicated to the restoration of images in fluorescence microscopy. Because no algorithm exists to perfectly correct those aberrations, we propose to implement several algorithms for each kind of problem, including the most common algorithms, which are well know and widely used, and some of the state of the art algorithms.<br />
<br />
Bold and Tag'ed with a #, working prototype available.<br />
<br />
Bold and tag'ed with a @, prototype expected on or before august<br />
<br />
=== preliminary work ===<br />
* '''fft convolution #''' ( [http://hdl.handle.net/10380/3154 Insight Journal publication] )<br />
Most of the deconvolution methods are based on multiple deconvolution or on FFT transforms. This preliminary work will be very useful to implement the deconvolution filters.<br />
* '''noise simulation #''' ( [http://hdl.handle.net/10380/3158 Insight Journal publication] )<br />
Being able to simulate the noise behavior is very important because it let the user compare the result of a restoration method with the known unblurred object.<br />
<br />
=== Deconvolution ===<br />
* non-blind deconvolution<br />
This is the most common deconvolution type. With all those methods, it is supposed that the point spread function is known. Most of those methods, for practical reasons, also assume that the point spread function (PSF) is spatially invariant in the image. Some of the methods are focused on the computation efficiency, at the cost of the restoration quality - often the linear algorithms -, and some on the restoration quality at the cost of the computation complexity - usually the iterative algorithms. The fluorescence noise follows a Poisson distribution, but is often considered as gaussian noise to simplify the computations. This assumption is generally valid when the SNR is high - most of the time for wide field microscopy. Because of the noise amplification produce by the deconvolution process, most of the methods are regularized. In fact, the only unregularized methods are iterative, and are effectively regularized by stopping the iteration process before the convergence.<br />
<br />
* Space invariant PSF - Linear algorithms<br />
All the proposed linear algorithms are made with the assumption of an additive gaussian noise. Other algorithms combined with wavelet transformed produce better results. <br />
<br />
# '''Regularized Linear Least Squares (truncated SVD) #'''<br />
# '''Maximum A Posteriori Linear Least Squares #'''<br />
# '''Wiener #'''<br />
# '''Tikhonov Miller #'''<br />
<br />
* Space Invariant - Iterative Algorithms<br />
# '''van Cittert #''': No noise assumption. A single convolution is required by iteration.<br />
# '''Jansson-van Cittert #''': This is a constrained version of the van Cittert algorithm. The pixel values are constrained in a range of values.<br />
# '''Landweber #''': The noise is assumed to follow a gaussian additive model. The algorithm requires two convolutions by iteration and the step size is fixed, which makes it converge slowly. It can be optionally constrained to avoid negative values as expected in fluorescence microscopy.<br />
# '''Richardson-Lucy #''': The noise is assumed to follow a poisson model. The algorithm requires two convolutions by iteration and the step size is fixed, which makes it converge slowly. The non negativity property is ensured without additional constraint. This algorithm is also known as Maximum Likelihood Maximization Expectation.<br />
# '''Damped Richardson-Lucy #''' This is a simple regularized version of the Richardson-Lucy algorithm. It is widely used in astronomy.<br />
# '''Tikhonov-Miller regularized Richardson-Lucy #''': This is a regularized version of the Richardson-Lucy algorithm using the Tikhonov-Miller usual penalization. Ref: Dey et al. 3D Microscopy Deconvolution using Richardson-Lucy Algorithm with Total Variation Regularization. hal.archives-ouvertes.fr (2004)<br />
# Total variation regularized Richardson-Lucy: This is a regularized version of the Richardson-Lucy algorithm which also minimize the Total Variation of the image to avoid the noise amplification.<br />
# '''Maximum Entropy regularized Richardson-Lucy #''': This is a regularized version of the Richardson lucy algoritm by imposing a maximum entropy constraint on the unblurred image.<br />
# Good regularized Richardson-Lucy: This is a regularize Richardson-Lucy algorithm which also minimize the Good's roughness.<br />
# '''Iterative Constrained Tikhonov-Miller @''': The noise is assumed to follow an additive gaussian model, and the process is regularized using the usual penalization. The non negativity is enforced at each iteration and the convergence is accelerated with a conjugate gradient acceleration. <br />
# Verveer's Maximum A Posteriori (MAPGG, MAPGE, MAPPG, MAPPE, MAPGR and MAPPR): The noise is assumed to follow either a gaussian or a poisson model. Three different a priori can be imposed on the unblurred image: a gaussian model, a maximum entroy or a Good's roughness. The process is accelerated with a Newton acceleration.<br />
# Markov Random Field MAP: The noise is assumed to follow a poisson model. The unblurred image is assumed to be a realization of a Markov random field. The problem is solved with a split gradient technique which is known to converge slowly, but the result quality is enhance compared to other state of the art algorithms.<br />
# Generalized Vector-Valued Total Variation: The noise is assumed to follow an additive gaussian model. The process also minimize the total variation and is accelerated. The code is available for matlab with a BSD license.<br />
* space variant psf<br />
# Depth-variant ML-EM<br />
* PSF<br />
The PSF is required for all the non-blind deconvolution methods. It is possible to get it either by measuring it with beads, are with a model. One way are the other both have their advantages and inconvenience and should be available for the final user.<br />
# PSF simulation<br />
# measurement / Evaluation of psf<br />
* Regularization Parameters Estimation<br />
# Generalized Cross Validation (GCV): A good estimation can be computed for the Tikhonov-Miller regularization with the generalized cross validation method.<br />
<br />
=== Usability ===<br />
On the implementation side, several goal should be reached.<br />
# '''observability #''': The iterative deconvolution algorithm are usually quite long to run - several minutes or tens of minutes on todays computers. As a consequence, it is important that the process can be observed by the user so that he can validate visually the intermediate results. The various measurements made should also be available during the process. If the result is not the expected one, or if the expected result is reach sooner than expected, the user should be able to interrupt the process cleanly.<br />
# '''continue a completed process to increase the number of iterations #''': The iterative filter should provide a mechanism to restart a completed deconvolution in order to increase the number of iterations.<br />
# '''preconditionning #''': Preconditionning is a usual technique where the blurred image and/or the PSF are transformed at the beginning at the deconvolution in order to improve the deconvolution quality or to decrease the number of iterations needed to reach the convergence. The usual precoditionning methods include the gaussian blurring, the Wiener fieltering and various denoising methods (mostly wavelet based).<br />
# multithreaded calculators: ITK does not currently provide any base class to easily implement multithreading in the calculators. We propose to implement such a base class and to use it in the calculators required in the other tasks.<br />
# '''FFTW wisdom integration #''': FFTW provides a mechanism to store the optimized plans on the disk. We propose to use this capability in ITK FFTW filters and to make it's usage transparent for the user.<br />
<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
The objectives of the project week is to share with the community the filters to come to avoid multiple groups working on the same algorithms. Persons interested can contact gaetan or alex directly. <br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
Transition as many filters as possible to the Insight Journal.<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
TBA<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
This work will be (eventually) delivered to the NA-MIC Kit as an<br />
#ITK Module<br />
<br />
<br />
==References==<br />
[01] Ref: Preza et al. Regularized method for reconstruction of three-dimensional microscopic objects from optical sections. Journal of the Optical Society of America (1992) vol. 9 (2) pp. 219-228<br><br />
[02] Ref: Preza et al. Image reconstruction for 3-D light microscopy with a regularized linear method incorporating a smoothness prior. Presented at the IS&T/SPIE Symposium on Electronic Imaging (1993) vol. 1905 (129-139)<br><br />
[03] Ref: Richardson. Bayesian-Based Iterative Method of Image Restoration. Journal of the Optical Society of America (1917-1983) (1972) vol. 62 pp. 55-+<br><br />
[04] Ref: Lucy. An iterative technique for the rectification of observed distributions. Astronomical Journal (1974) vol. 79 pp. 745-+<br><br />
[05] Ref: White. Image Restoration Using the Damped Richardson-Lucy Iteration. Proceedings (1994) vol. 61 pp. 292-+<br><br />
[06] Ref: Dey et al. 3D Microscopy Deconvolution using Richardson-Lucy Algorithm with Total Variation Regularization. hal.archives-ouvertes.fr (2004)<br><br />
[07] Ref: Monvel et al. Image Restoration for Confocal Microscopy: Improving the Limits of Deconvolution, with Application to the Visualization of the Mammalian Hearing Organ. Biophysical Journal (2001)<br><br />
[08] Ref: Verveer et Jovin. Acceleration of the ICTM image restoration algorithm. Journal of Microscopy (1997) (188) pp. 191–195<br><br />
[09] Ref: Verveer. Computational and Optical Methods for Improving Resolution and Signal Quality in Fluorescence Microscopy. adsabs.harvard.edu (1998)<br><br />
[10] Ref: Vicidomini et al. Application of the split-gradient method to 3D image deconvolution in fluorescence microscopy. Journal of Microscopy (2009) vol. 234 (1) pp. 47-61<br><br />
[11] Ref: P. Rodriguez, B. Wohlberg, "Efficient Minimization Method for a Generalized Total Variation Functional" IEEE Transactions on Image Processing, 2009, 18:2(322-332)<br><br />
[12] Ref: Preza et Conchello. Depth-variant maximum-likelihood restoration for three-dimensional fluorescence microscopy. Journal of the Optical Society of America A (2004) vol. 21 (9) pp. 1593-1601<br><br />
[13] Ref: Agard. Optical sectioning microscopy: cellular architecture in three dimensions. Annual review of Biophysics and Bioengineering (1984) vol. 13 pp. 191-219<br><br />
[14] Ref: Gibson et Lanni. Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy. J. Opt. Soc. Am. A (1992) vol. 9 (1) pp. 154-166<br><br />
[15] Ref: Haeberle. Focusing of light through a stratified medium: a practical approach for computing microscope point spread functions. Part I: Conventional microscopy. Optics Communications (2003) vol. 216 (1-3) pp. 55 - 63<br><br />
[16] Ref: Haeberle. Focusing of light through a stratified medium: a practical approach for computing microscope point spread functions: Part II: confocal and multiphoton microscopy. Optics Communications (2004) vol. 235 (1-3) pp. 1 - 10<br><br />
[17] Ref: Dey et al. 3D Microscopy Deconvolution using Richardson-Lucy Algorithm with Total Variation Regularization. hal.archives-ouvertes.fr (2004)<br><br />
[18] Ref: Van Kempen et al. A quantitative comparison of image restoration methods for confocal microscopy. Journal of Microscopy (1997) vol. 185 (3) pp. 354-365<br><br />
<br />
</div></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Project_Week_DICOM_supplement_145&diff=537932010 Project Week DICOM supplement 1452010-06-14T05:37:38Z<p>Agouaillard: /* Project */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Mathieu Malaterre: CoSMo Software<br />
* Alex. Gouaillard: CoSMo SOftware, A*STAR<br />
* NAMIC: (luis?)<br />
<br />
==Project==<br />
DICOM Supplement 145 provide a way to go over the 32bits limits and allow storing of large images. We propose to implement this specification.<br />
In addition, we would implement DICOM specification for JPEG 2000 Part 2 Multi-component Image Compression. This portion of the standard provides higher<br />
compression ratio for storing multicomponent images. <br />
Finally by implementing DICOM supplement 132, we would provides support for storing of surfaces and 3D volumes, as an addition to the 2D RTSTRUCT.<br />
<br />
<br />
=== Standard support for Large multicomponent images in ITK ===<br />
DICOM currently defines Image IODs by storing the rows and columns as unsigned short<br />
integer. This means that an image can only be at most of size 2^16 * 2^16 pixels.<br />
This is a limitation for Microscopy Images as , for example, typical Whole Slice Images an be 60,000 * 80,000 pixels. Since images are generally stored with 24-bit color<br />
pixels, this means WSI can go up to 15Gb. Confocal Microscopy Images add one additional<br />
dimension, and are today already capable of acquiring 24 channels. They are reported to need up<br />
to petabytes.<br />
For this reason DICOM Supplement 145 defines a way to store images into multiple<br />
DICOM files providing a mean to work around this 32bits limitation of DICOM.<br />
By implementing this Supplement (which is still in Ballot), we would provide to the<br />
ITK community a proof of concept and allow people to start saving larges images using DICOM.<br />
This would allow the re-using of technologies and prevent people from re-inventing the wheel<br />
and start using a new file format to exchange medical image (second system effect). <br />
<br />
<br />
<br />
=== Standard support for multicomponent images compression in ITK ===<br />
Microscopy Images, on top of being larger sometimes by several orders of magnitudes from medical images, are also multi-component. Even though ITK handle multicomponent images per say, by defining the right pixel type, nothing is available today for the storage and compression of images that would have more than 3 channels (RGB). Since 2001, the DICOM standard allows JPEG 2000 compression. GDCM 2.x has supported a portion of the standard by providing an API to allow transfer syntax such as JPEG 2000 Image Compression (1.2.840.10008.1.2.4.90 and 1.2.840.10008.1.2.4.91). However the standard also includes JPEG 2000 Part 2 Multi-component Image Compression (1.2.840.10008.1.2.4.92 and 1.2.840.10008.1.2.4.93). The latter has never made into GDCM / ITK, or any other open source DICOM toolkit, since as quoted from the presentation: “Image Compression Refresher – JPEG 2000 and 3D, David Clunie”: the compression gain was modest (using lossless compression). We see now an opportunity that this compression can make it into GDCM / ITK since microscopy images would perfectly fit into the original design of the compression (ISO/IEC 15444-2:2003 Annex J). This would ease the dissemination of large dataset by reusing standard compression techniques, since this would greatly reduce the size of those file datasets. This will be particularly useful for microscopic images. At the time of writing no other open-source DICOM toolkit offer this compression algorithm. <br />
<br />
<br />
<br />
=== Standard support for discrete 2 and 3 manifold storage in ITK ===<br />
From its early design, ITK has always offered some n-dimensional n-manifold (polygonal meshes) support through the itk::Mesh class. However at the time of writing of this proposal, there is still no official way to read or write those meshes from and to a filesystem in ITK. Only an hybrid solution is available in Insight Applications. However it implies a dependency to the entire VTK library which is an overkill most of the time.<br />
Thanks to the work on itk::QuadEdgeMesh some progress have been made toward that goal. The Review directory surrently holds a very simple VTK PolyData reader and writer. However, it only supports legacy vtk files using ASCII encoding. For its defense, this implementation was only made for regression testing and illustration of the filters usage.<br />
We are proposing here to fill this gap in the ITK toolkit and implement DICOM's Supplement 132, part of the standard since 2008, which would add surfaces and volumes meshes (2 and 3 manifolds) storage capacity to GDCM /ITK. This would add support for surfaces and volume (2 and 3 manifolds in n dimensional space, see supplemental material annex).<br />
We suggest 2 different options. The first option would allow for storage of itk::QuadEdgeMesh as a DICOM file. The second options would allow for storage of an itk::Mesh as a DICOM file. Of course reading the corresponding structures from a DICOM file would also be provided.<br />
As an illustration, we make a clear distinction in what itk::QuadEdgeMesh handles and what itk::Mesh can handle. Both 2 and 3 manifold objects are handled in the DICOM standard.<br />
We do anticipate a large portion of this task to be validation testing. Since there are no other serialization mechanism available in ITK, we will need to setup an hybrid system with VTK to perform validation on the dataset written (a 3D VTK mesh will be used as input for the tests). For this we would be re-using code from InsightApplications/Auxiliary/vtk/vtk2itk.cxx.<br />
<br />
<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
The objectives of the project week is to share with the community and make a list of persons interested and of corresponding efforts before we start implementing. Typically at the end of the week we would like to have identified existing parts, ongoing effort and have a roadmap available possibly with other groups joining in depending on needs, manpower and expertise.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a<br />
<br />
* ITK Module<br />
* Other: GDCM extension (gdcm is included in ITK)<br />
<br />
==References==<br />
*the official DICOM Standard Proposal [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf here]<br />
<br />
</div></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week_Microscopy_extensions_for_ITK&diff=537922010 Summer Project Week Microscopy extensions for ITK2010-06-14T05:34:50Z<p>Agouaillard: Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Back to Projects List </gallery> ==Key Investigators== * Gaetan lehmann: INRA * Alex Gouaillard: C…'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Back to Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Gaetan lehmann: INRA<br />
* Alex Gouaillard: CoSMo Software / A*STAR<br />
* NAMIC: (luis?)<br />
<br />
<br />
== Introduction ==<br />
Fluorescence microscopy is a very common image acquisition modality, used in many fields including medical imaging and biological research. Depending on the techniques used, the images produced can be in 2D or 3D, time lapse, and contain several channels.<br />
ITK provides a lot of useful tools to analyze the images produce in fluorescence microscopy. The N-dimensionality of ITK is especially useful when dealing with 3D data sets. However, it contains very few methods to correct the aberrations introduced in the image during the acquisition.<br />
We propose to implement some tools dedicated to the restoration of images in fluorescence microscopy. Because no algorithm exists to perfectly correct those aberrations, we propose to implement several algorithms for each kind of problem, including the most common algorithms, which are well know and widely used, and some of the state of the art algorithms.<br />
<br />
Bold and Tag'ed with a #, working prototype available.<br />
<br />
Bold and tag'ed with a @, prototype expected on or before august<br />
<br />
=== preliminary work ===<br />
* '''fft convolution #''' ( [http://hdl.handle.net/10380/3154 Insight Journal publication] )<br />
Most of the deconvolution methods are based on multiple deconvolution or on FFT transforms. This preliminary work will be very useful to implement the deconvolution filters.<br />
* '''noise simulation #''' ( [http://hdl.handle.net/10380/3158 Insight Journal publication] )<br />
Being able to simulate the noise behavior is very important because it let the user compare the result of a restoration method with the known unblurred object.<br />
<br />
=== Deconvolution ===<br />
* non-blind deconvolution<br />
This is the most common deconvolution type. With all those methods, it is supposed that the point spread function is known. Most of those methods, for practical reasons, also assume that the point spread function (PSF) is spatially invariant in the image. Some of the methods are focused on the computation efficiency, at the cost of the restoration quality - often the linear algorithms -, and some on the restoration quality at the cost of the computation complexity - usually the iterative algorithms. The fluorescence noise follows a Poisson distribution, but is often considered as gaussian noise to simplify the computations. This assumption is generally valid when the SNR is high - most of the time for wide field microscopy. Because of the noise amplification produce by the deconvolution process, most of the methods are regularized. In fact, the only unregularized methods are iterative, and are effectively regularized by stopping the iteration process before the convergence.<br />
<br />
* Space invariant PSF - Linear algorithms<br />
All the proposed linear algorithms are made with the assumption of an additive gaussian noise. Other algorithms combined with wavelet transformed produce better results. <br />
<br />
# '''Regularized Linear Least Squares (truncated SVD) #'''<br />
# '''Maximum A Posteriori Linear Least Squares #'''<br />
# '''Wiener #'''<br />
# '''Tikhonov Miller #'''<br />
<br />
* Space Invariant - Iterative Algorithms<br />
# '''van Cittert #''': No noise assumption. A single convolution is required by iteration.<br />
# '''Jansson-van Cittert #''': This is a constrained version of the van Cittert algorithm. The pixel values are constrained in a range of values.<br />
# '''Landweber #''': The noise is assumed to follow a gaussian additive model. The algorithm requires two convolutions by iteration and the step size is fixed, which makes it converge slowly. It can be optionally constrained to avoid negative values as expected in fluorescence microscopy.<br />
# '''Richardson-Lucy #''': The noise is assumed to follow a poisson model. The algorithm requires two convolutions by iteration and the step size is fixed, which makes it converge slowly. The non negativity property is ensured without additional constraint. This algorithm is also known as Maximum Likelihood Maximization Expectation.<br />
# '''Damped Richardson-Lucy #''' This is a simple regularized version of the Richardson-Lucy algorithm. It is widely used in astronomy.<br />
# '''Tikhonov-Miller regularized Richardson-Lucy #''': This is a regularized version of the Richardson-Lucy algorithm using the Tikhonov-Miller usual penalization. Ref: Dey et al. 3D Microscopy Deconvolution using Richardson-Lucy Algorithm with Total Variation Regularization. hal.archives-ouvertes.fr (2004)<br />
# Total variation regularized Richardson-Lucy: This is a regularized version of the Richardson-Lucy algorithm which also minimize the Total Variation of the image to avoid the noise amplification.<br />
# '''Maximum Entropy regularized Richardson-Lucy #''': This is a regularized version of the Richardson lucy algoritm by imposing a maximum entropy constraint on the unblurred image.<br />
# Good regularized Richardson-Lucy: This is a regularize Richardson-Lucy algorithm which also minimize the Good's roughness.<br />
# '''Iterative Constrained Tikhonov-Miller @''': The noise is assumed to follow an additive gaussian model, and the process is regularized using the usual penalization. The non negativity is enforced at each iteration and the convergence is accelerated with a conjugate gradient acceleration. <br />
# Verveer's Maximum A Posteriori (MAPGG, MAPGE, MAPPG, MAPPE, MAPGR and MAPPR): The noise is assumed to follow either a gaussian or a poisson model. Three different a priori can be imposed on the unblurred image: a gaussian model, a maximum entroy or a Good's roughness. The process is accelerated with a Newton acceleration.<br />
# Markov Random Field MAP: The noise is assumed to follow a poisson model. The unblurred image is assumed to be a realization of a Markov random field. The problem is solved with a split gradient technique which is known to converge slowly, but the result quality is enhance compared to other state of the art algorithms.<br />
# Generalized Vector-Valued Total Variation: The noise is assumed to follow an additive gaussian model. The process also minimize the total variation and is accelerated. The code is available for matlab with a BSD license.<br />
* space variant psf<br />
# Depth-variant ML-EM<br />
* PSF<br />
The PSF is required for all the non-blind deconvolution methods. It is possible to get it either by measuring it with beads, are with a model. One way are the other both have their advantages and inconvenience and should be available for the final user.<br />
# PSF simulation<br />
# measurement / Evaluation of psf<br />
* Regularization Parameters Estimation<br />
# Generalized Cross Validation (GCV): A good estimation can be computed for the Tikhonov-Miller regularization with the generalized cross validation method.<br />
<br />
=== Usability ===<br />
On the implementation side, several goal should be reached.<br />
# '''observability #''': The iterative deconvolution algorithm are usually quite long to run - several minutes or tens of minutes on todays computers. As a consequence, it is important that the process can be observed by the user so that he can validate visually the intermediate results. The various measurements made should also be available during the process. If the result is not the expected one, or if the expected result is reach sooner than expected, the user should be able to interrupt the process cleanly.<br />
# '''continue a completed process to increase the number of iterations #''': The iterative filter should provide a mechanism to restart a completed deconvolution in order to increase the number of iterations.<br />
# '''preconditionning #''': Preconditionning is a usual technique where the blurred image and/or the PSF are transformed at the beginning at the deconvolution in order to improve the deconvolution quality or to decrease the number of iterations needed to reach the convergence. The usual precoditionning methods include the gaussian blurring, the Wiener fieltering and various denoising methods (mostly wavelet based).<br />
# multithreaded calculators: ITK does not currently provide any base class to easily implement multithreading in the calculators. We propose to implement such a base class and to use it in the calculators required in the other tasks.<br />
# '''FFTW wisdom integration #''': FFTW provides a mechanism to store the optimized plans on the disk. We propose to use this capability in ITK FFTW filters and to make it's usage transparent for the user.<br />
<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
TBA<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
This work will be (eventually) delivered to the NA-MIC Kit as an<br />
#ITK Module<br />
<br />
<br />
==References==<br />
[01] Ref: Preza et al. Regularized method for reconstruction of three-dimensional microscopic objects from optical sections. Journal of the Optical Society of America (1992) vol. 9 (2) pp. 219-228<br><br />
[02] Ref: Preza et al. Image reconstruction for 3-D light microscopy with a regularized linear method incorporating a smoothness prior. Presented at the IS&T/SPIE Symposium on Electronic Imaging (1993) vol. 1905 (129-139)<br><br />
[03] Ref: Richardson. Bayesian-Based Iterative Method of Image Restoration. Journal of the Optical Society of America (1917-1983) (1972) vol. 62 pp. 55-+<br><br />
[04] Ref: Lucy. An iterative technique for the rectification of observed distributions. Astronomical Journal (1974) vol. 79 pp. 745-+<br><br />
[05] Ref: White. Image Restoration Using the Damped Richardson-Lucy Iteration. Proceedings (1994) vol. 61 pp. 292-+<br><br />
[06] Ref: Dey et al. 3D Microscopy Deconvolution using Richardson-Lucy Algorithm with Total Variation Regularization. hal.archives-ouvertes.fr (2004)<br><br />
[07] Ref: Monvel et al. Image Restoration for Confocal Microscopy: Improving the Limits of Deconvolution, with Application to the Visualization of the Mammalian Hearing Organ. Biophysical Journal (2001)<br><br />
[08] Ref: Verveer et Jovin. Acceleration of the ICTM image restoration algorithm. Journal of Microscopy (1997) (188) pp. 191–195<br><br />
[09] Ref: Verveer. Computational and Optical Methods for Improving Resolution and Signal Quality in Fluorescence Microscopy. adsabs.harvard.edu (1998)<br><br />
[10] Ref: Vicidomini et al. Application of the split-gradient method to 3D image deconvolution in fluorescence microscopy. Journal of Microscopy (2009) vol. 234 (1) pp. 47-61<br><br />
[11] Ref: P. Rodriguez, B. Wohlberg, "Efficient Minimization Method for a Generalized Total Variation Functional" IEEE Transactions on Image Processing, 2009, 18:2(322-332)<br><br />
[12] Ref: Preza et Conchello. Depth-variant maximum-likelihood restoration for three-dimensional fluorescence microscopy. Journal of the Optical Society of America A (2004) vol. 21 (9) pp. 1593-1601<br><br />
[13] Ref: Agard. Optical sectioning microscopy: cellular architecture in three dimensions. Annual review of Biophysics and Bioengineering (1984) vol. 13 pp. 191-219<br><br />
[14] Ref: Gibson et Lanni. Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy. J. Opt. Soc. Am. A (1992) vol. 9 (1) pp. 154-166<br><br />
[15] Ref: Haeberle. Focusing of light through a stratified medium: a practical approach for computing microscope point spread functions. Part I: Conventional microscopy. Optics Communications (2003) vol. 216 (1-3) pp. 55 - 63<br><br />
[16] Ref: Haeberle. Focusing of light through a stratified medium: a practical approach for computing microscope point spread functions: Part II: confocal and multiphoton microscopy. Optics Communications (2004) vol. 235 (1-3) pp. 1 - 10<br><br />
[17] Ref: Dey et al. 3D Microscopy Deconvolution using Richardson-Lucy Algorithm with Total Variation Regularization. hal.archives-ouvertes.fr (2004)<br><br />
[18] Ref: Van Kempen et al. A quantitative comparison of image restoration methods for confocal microscopy. Journal of Microscopy (1997) vol. 185 (3) pp. 354-365<br><br />
<br />
</div></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week&diff=537912010 Summer Project Week2010-06-14T04:22:33Z<p>Agouaillard: /* Microscopy Image Analysis */</p>
<hr />
<div>__NOTOC__<br />
<br />
Back to [[Project Events]], [[Events]]<br />
<br />
[[Image:PW-MIT2010.png|300px]]<br />
<br />
<br />
==Background==<br />
<br />
We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. <br />
<br />
Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br />
<br />
The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br />
<br />
This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
== Logistics ==<br />
*'''Dates:''' June 21-25, 2010<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.<br />
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). <br />
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process. <br />
<br />
''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''<br />
''' $189/night/room (plus tax).'''<br />
''' This rate is good only through June 1.'''<br />
<br />
Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290. <br />
<br />
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br />
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]<br />
<br />
==Agenda==<br />
=== Monday, June 21, 2010 === <br />
** noon-1pm lunch <br />
**1pm: Welcome (Ron Kikinis)<br />
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template]) <br />
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)<br />
<br />
=== Tuesday, June 22, 2010 ===<br />
** 8:30am breakfast<br />
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.<br />
**9:45-10:30am 3D Slicer Update (Steve Pieper)<br />
**10:30-11am OpenIGTLink Update (Junichi Tokuda)<br />
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)<br />
** noon lunch <br />
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)<br />
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]<br />
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)<br />
** 5:30pm adjourn for day<br />
<br />
=== Wednesday, June 23, 2010 ===<br />
** 8:30am breakfast<br />
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)<br />
** noon lunch<br />
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]<br />
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)<br />
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanez)<br />
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)<br />
** 5:30pm adjourn for day<br />
<br />
=== Thursday, June 24, 2010 ===<br />
** 8:30am breakfast<br />
<br />
** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]<br />
** noon lunch<br />
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)<br />
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)<br />
** 5:30pm adjourn for day<br />
<br />
=== Friday, June 25, 2010 === <br />
** 8:30am breakfast<br />
** 10am-noon: [[#Projects|Project Progress Updates]]<br />
*** Noon: Lunch boxes and adjourn by 1:30pm.<br />
***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br />
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br />
***Next Project Week [[AHM_2011|in Utah]]<br />
<br />
==Projects==<br />
<br />
<br />
<br />
=== Segmentation ===<br />
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)<br />
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)<br />
*[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)<br />
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)<br />
*[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)<br />
*[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)<br />
*[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)<br />
*[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)<br />
*[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)<br />
<br />
=== Registration ===<br />
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)<br />
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)<br />
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)<br />
*[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)<br />
*[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)<br />
*[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)<br />
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)<br />
<br />
=== IGT ===<br />
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)<br />
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi)<br />
* Liver Ablation (Haiying Liu)<br />
* [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)<br />
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)<br />
* [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)<br />
*[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)<br />
*[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)<br />
<br />
=== Radiotherapy ===<br />
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)<br />
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)<br />
*[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )<br />
<br />
=== Analysis ===<br />
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)<br />
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)<br />
*[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)<br />
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)<br />
<br />
===[[Microscopy Image Analysis]] ===<br />
* [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)<br />
* [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK ]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )<br />
* [[ 2010 Summer Project Week Flow Cytometry | Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)<br />
* [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)<br />
* [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)<br />
* [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)<br />
* [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)<br />
* [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)<br />
* [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)<br />
* [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)<br />
* [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)<br />
<br />
=== Shape Analysis ===<br />
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)<br />
* [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)<br />
* [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)<br />
<br />
=== Informatics ===<br />
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)<br />
<br />
=== Diffusion ===<br />
*[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)<br />
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)<br />
*[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)<br />
*[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)<br />
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)<br />
*[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)<br />
<br />
=== NA-MIC Kit Internals ===<br />
*Module Inventory (Steve, Jim)<br />
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)<br />
* [[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)<br />
*[[2010_NAMIC_Project_week:XNATE_Client_For_Slicer|XNAT Enterprise webservices client for Slicer]] (Wendy Plesniak, Mark Anderson)<br />
*[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)<br />
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)<br />
<br />
*[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)<br />
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)<br />
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)<br />
<br />
== Preparation ==<br />
<br />
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br />
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!<br />
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
# People doing Slicer related projects should come to project week with slicer built on your laptop.<br />
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).<br />
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br />
<br />
==Attendee List==<br />
<br />
<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font> <br />
<br />
# Nicole Aucoin , BWH<br />
# Michel Audette , Kitware<br />
# Stephen Aylward , Kitware, Inc<br />
# Alexis Boucharin , UNC Neuro Image Research and Analysis Laboratories<br />
# Sylvain Bouix , BWH<br />
# Michael Bowers , Johns Hopkins University<br />
# Francois Budin , UNC<br />
# Everette Burdette , Acoustic MedSystems, Inc.<br />
# Laurent CHAUVIN , Brigham and Women's Hospital<br />
# Min Chen , Johns Hopkins University<br />
# Jason Crane , UCSF<br />
# Manasi Datar , SCI Institute<br />
# Liya Ding , The Ohio State University<br />
# Ryan Eckbo , BWH<br />
# Ilker Ersoy , University of Missouri Columbia<br />
# Andriy Fedorov , Surgical Planning Lab<br />
# Jean-Christophe Fillion-Robin , Kitware Inc.<br />
# Julien Finet , Kitware Inc<br />
# James Fishbaugh , SCI Institute<br />
# Karl Fritscher , UMIT<br />
# Yi Gao , Gerogia Tech<br />
# Arnaud GELAS , Harvard Medical School<br />
# Chris Gorgolewski , SPL<br />
# alexandre gouaillard , CoSMo Software<br />
# Sylvain Gouttard , SCI Institute<br />
# Kedar Grama, Rensselaer Polytechnic Institute<br />
# Daniel Haehn , University of Pennsylvania<br />
# Adel Hafiane , ENSI-Bourges<br />
# Nathan Hageman , <br />
# Dieter Hahn , University Erlangen<br />
# Michael Halle , BWH/SPL<br />
# Corentin Hamel , UNC Chapel Hill<br />
# Nobuhiko Hata , Brigham and Women's Hospital<br />
# Kathryn Hayes , Brigham and Women's Hospital<br />
# Nicholas Herlambang , AZE, Ltd.<br />
# Leslie Holton , Medtronic Navigation<br />
# Luis Ibanez , KITWARE Inc.<br />
# Jayender Jagadeesan , SPL<br />
# Hans Johnson , University of Iowa<br />
# Tina Kapur , Brigham and Women's Hospital<br />
# Ron Kikinis , Brigham and Women's Hospital<br />
# Minjeong Kim , UNC-Chapel Hill<br />
# Ivan Kolesov , Georgia Institute of Technology<br />
# Garrett Larson , UNC-CH<br />
# Rui Li , MGH<br />
# Curtis Lisle , KnowledgeVis, LLC<br />
# Haiying Liu , Brigham and Women's Hospital<br />
# Yanling Liu , SAIC-Frederick, Inc.<br />
# Bradley Lowekamp , Lockheed Martin<br />
# raghu machiraju , The Ohio State University<br />
# Vincent Magnotta , The University of Iowa<br />
# mathieu malaterre , CoSMo Software<br />
# Daniel Marcus , Washington University<br />
# Katie Mastrogiacomo , Brigham and Women's Hospital<br />
# Joy Matsui , University<br />
# Sean Megason , Harvard Medical School<br />
# Dominik Meier , BWH, Boston MA<br />
# bjoern menze , CSAIL MIT<br />
# Mikhail Milchenko , WUSTL<br />
# James Miller , GE Research<br />
# Kishore Mosaliganti , Harvard Medical School<br />
# Marc Niethammer , UNC Chapel Hill<br />
# Isaiah Norton , BWH Neurosurgery<br />
# Raghav Padmanabhan , RPI<br />
# Kannappan Palaniappan , university of Missouri<br />
# Beatriz Paniagua , University of North Caolina at Chapel Hill<br />
# Xenophon Papademetris , Yale University<br />
# David Partyka , Kitware Inc<br />
# Pratik Patel , <br />
# Sudhir Pathak , Univeristy Of Pittsburgh<br />
# Marta Peroni , Politecnico di Milano<br />
# Antonin Perrot-Audet , Harvard Medical School<br />
# Steve Pieper , Isomics, Inc.<br />
# Wendy Plesniak , BWH<br />
# Kilian Pohl , IBM<br />
# Sonia Pujol , Brigham and Women's Hospital<br />
# Nicolas Rannou , Harvard Medical School<br />
# Tammy Riklin Raviv , MIT, CSAIL<br />
# Marco Ruiz , UCSD<br />
# William Schroeder , Kitware<br />
# Mark Scully , The Mind Research Network<br />
# Greg Sharp , MGH<br />
# Yundi Shi , UNC Chapel Hill<br />
# Nadya Shusharina , MGH<br />
# Shantanu Singh , The Ohio State University<br />
# Gareth Smith , Wolfson Medical Imaging Centre (WMIC)<br />
# Lydie Souhait , Harvard Medical School<br />
# Dominik Spinczyk , Silesian University of Technology<br />
# Padmapriya Srinivasan , <br />
# Xiaodong Tao , GE Research<br />
# Junichi Tokuda , Brigham and Women's Hospital<br />
# Tamas Ungi , Queen's University<br />
# Clement Vachet , UNC Chapel Hill<br />
# Gopalkrishna Veni , SCI Institute<br />
# Demian Wassermann , SPL/LMI/PNL<br />
# Adam Weinrich , Nokia<br />
# Sandy Wells , BWH<br />
# Guorong Wu , University of North Carolina at Chapel Hill<br />
# Alexander Yarmarkovich , ISOMICS<br />
# Alexander Zaitsev , Brigham and Womens Hospital</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Project_Week_DICOM_supplement_145&diff=537902010 Project Week DICOM supplement 1452010-06-14T04:18:59Z<p>Agouaillard: /* Delivery Mechanism */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Mathieu Malaterre: CoSMo Software<br />
* Alex. Gouaillard: CoSMo SOftware, A*STAR<br />
* NAMIC: (luis?)<br />
<br />
==Project==<br />
DICOM Supplement 145 provide a way to go over the 32bits limits and allow storing of large images. We propose to implement this specification.<br />
In addition, we would implement DICOM specification for JPEG 2000 Part 2 Multi-component Image Compression. This portion of the standard provides higher<br />
compression ratio for storing multicomponent images. <br />
Finally by implementing DICOM supplement 132, we would provides support for storing of surfaces and 3D volumes, as an addition to the 2D RTSTRUCT.<br />
<br />
<br />
<br />
DICOM currently defines Image IODs by storing the rows and columns as unsigned short<br />
integer. This means that an image can only be at most of size 2^16 * 2^16 pixels.<br />
This is a limitation for Microscopy Images as , for example, typical Whole Slice Images an be 60,000 * 80,000 pixels. Since images are generally stored with 24-bit color<br />
pixels, this means WSI can go up to 15Gb. Confocal Microscopy Images add one additional<br />
dimension, and are today already capable of acquiring 24 channels. They are reported to need up<br />
to petabytes.<br />
For this reason DICOM Supplement 145 defines a way to store images into multiple<br />
DICOM files providing a mean to work around this 32bits limitation of DICOM.<br />
By implementing this Supplement (which is still in Ballot), we would provide to the<br />
ITK community a proof of concept and allow people to start saving larges images using DICOM.<br />
This would allow the re-using of technologies and prevent people from re-inventing the wheel<br />
and start using a new file format to exchange medical image (second system effect). <br />
<br />
<br />
<br />
<br />
Microscopy Images, on top of being larger sometimes by several orders of magnitudes from medical images, are also multi-component. Even though ITK handle multicomponent images per say, by defining the right pixel type, nothing is available today for the storage and compression of images that would have more than 3 channels (RGB). Since 2001, the DICOM standard allows JPEG 2000 compression. GDCM 2.x has supported a portion of the standard by providing an API to allow transfer syntax such as JPEG 2000 Image Compression (1.2.840.10008.1.2.4.90 and 1.2.840.10008.1.2.4.91). However the standard also includes JPEG 2000 Part 2 Multi-component Image Compression (1.2.840.10008.1.2.4.92 and 1.2.840.10008.1.2.4.93). The latter has never made into GDCM / ITK, or any other open source DICOM toolkit, since as quoted from the presentation: “Image Compression Refresher – JPEG 2000 and 3D, David Clunie”: the compression gain was modest (using lossless compression). We see now an opportunity that this compression can make it into GDCM / ITK since microscopy images would perfectly fit into the original design of the compression (ISO/IEC 15444-2:2003 Annex J). This would ease the dissemination of large dataset by reusing standard compression techniques, since this would greatly reduce the size of those file datasets. This will be particularly useful for microscopic images. At the time of writing no other open-source DICOM toolkit offer this compression algorithm. <br />
<br />
<br />
<br />
<br />
From its early design, ITK has always offered some n-dimensional n-manifold (polygonal meshes) support through the itk::Mesh class. However at the time of writing of this proposal, there is still no official way to read or write those meshes from and to a filesystem in ITK. Only an hybrid solution is available in Insight Applications. However it implies a dependency to the entire VTK library which is an overkill most of the time.<br />
Thanks to the work on itk::QuadEdgeMesh some progress have been made toward that goal. The Review directory surrently holds a very simple VTK PolyData reader and writer. However, it only supports legacy vtk files using ASCII encoding. For its defense, this implementation was only made for regression testing and illustration of the filters usage.<br />
We are proposing here to fill this gap in the ITK toolkit and implement DICOM's Supplement 132, part of the standard since 2008, which would add surfaces and volumes meshes (2 and 3 manifolds) storage capacity to GDCM /ITK. This would add support for surfaces and volume (2 and 3 manifolds in n dimensional space, see supplemental material annex).<br />
We suggest 2 different options. The first option would allow for storage of itk::QuadEdgeMesh as a DICOM file. The second options would allow for storage of an itk::Mesh as a DICOM file. Of course reading the corresponding structures from a DICOM file would also be provided.<br />
As an illustration, we make a clear distinction in what itk::QuadEdgeMesh handles and what itk::Mesh can handle. Both 2 and 3 manifold objects are handled in the DICOM standard.<br />
We do anticipate a large portion of this task to be validation testing. Since there are no other serialization mechanism available in ITK, we will need to setup an hybrid system with VTK to perform validation on the dataset written (a 3D VTK mesh will be used as input for the tests). For this we would be re-using code from InsightApplications/Auxiliary/vtk/vtk2itk.cxx.<br />
<br />
<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
The objectives of the project week is to share with the community and make a list of persons interested and of corresponding efforts before we start implementing. Typically at the end of the week we would like to have identified existing parts, ongoing effort and have a roadmap available possibly with other groups joining in depending on needs, manpower and expertise.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a<br />
<br />
* ITK Module<br />
* Other: GDCM extension (gdcm is included in ITK)<br />
<br />
==References==<br />
*the official DICOM Standard Proposal [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf here]<br />
<br />
</div></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Project_Week_DICOM_supplement_145&diff=537892010 Project Week DICOM supplement 1452010-06-14T04:18:24Z<p>Agouaillard: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Mathieu Malaterre: CoSMo Software<br />
* Alex. Gouaillard: CoSMo SOftware, A*STAR<br />
* NAMIC: (luis?)<br />
<br />
==Project==<br />
DICOM Supplement 145 provide a way to go over the 32bits limits and allow storing of large images. We propose to implement this specification.<br />
In addition, we would implement DICOM specification for JPEG 2000 Part 2 Multi-component Image Compression. This portion of the standard provides higher<br />
compression ratio for storing multicomponent images. <br />
Finally by implementing DICOM supplement 132, we would provides support for storing of surfaces and 3D volumes, as an addition to the 2D RTSTRUCT.<br />
<br />
<br />
<br />
DICOM currently defines Image IODs by storing the rows and columns as unsigned short<br />
integer. This means that an image can only be at most of size 2^16 * 2^16 pixels.<br />
This is a limitation for Microscopy Images as , for example, typical Whole Slice Images an be 60,000 * 80,000 pixels. Since images are generally stored with 24-bit color<br />
pixels, this means WSI can go up to 15Gb. Confocal Microscopy Images add one additional<br />
dimension, and are today already capable of acquiring 24 channels. They are reported to need up<br />
to petabytes.<br />
For this reason DICOM Supplement 145 defines a way to store images into multiple<br />
DICOM files providing a mean to work around this 32bits limitation of DICOM.<br />
By implementing this Supplement (which is still in Ballot), we would provide to the<br />
ITK community a proof of concept and allow people to start saving larges images using DICOM.<br />
This would allow the re-using of technologies and prevent people from re-inventing the wheel<br />
and start using a new file format to exchange medical image (second system effect). <br />
<br />
<br />
<br />
<br />
Microscopy Images, on top of being larger sometimes by several orders of magnitudes from medical images, are also multi-component. Even though ITK handle multicomponent images per say, by defining the right pixel type, nothing is available today for the storage and compression of images that would have more than 3 channels (RGB). Since 2001, the DICOM standard allows JPEG 2000 compression. GDCM 2.x has supported a portion of the standard by providing an API to allow transfer syntax such as JPEG 2000 Image Compression (1.2.840.10008.1.2.4.90 and 1.2.840.10008.1.2.4.91). However the standard also includes JPEG 2000 Part 2 Multi-component Image Compression (1.2.840.10008.1.2.4.92 and 1.2.840.10008.1.2.4.93). The latter has never made into GDCM / ITK, or any other open source DICOM toolkit, since as quoted from the presentation: “Image Compression Refresher – JPEG 2000 and 3D, David Clunie”: the compression gain was modest (using lossless compression). We see now an opportunity that this compression can make it into GDCM / ITK since microscopy images would perfectly fit into the original design of the compression (ISO/IEC 15444-2:2003 Annex J). This would ease the dissemination of large dataset by reusing standard compression techniques, since this would greatly reduce the size of those file datasets. This will be particularly useful for microscopic images. At the time of writing no other open-source DICOM toolkit offer this compression algorithm. <br />
<br />
<br />
<br />
<br />
From its early design, ITK has always offered some n-dimensional n-manifold (polygonal meshes) support through the itk::Mesh class. However at the time of writing of this proposal, there is still no official way to read or write those meshes from and to a filesystem in ITK. Only an hybrid solution is available in Insight Applications. However it implies a dependency to the entire VTK library which is an overkill most of the time.<br />
Thanks to the work on itk::QuadEdgeMesh some progress have been made toward that goal. The Review directory surrently holds a very simple VTK PolyData reader and writer. However, it only supports legacy vtk files using ASCII encoding. For its defense, this implementation was only made for regression testing and illustration of the filters usage.<br />
We are proposing here to fill this gap in the ITK toolkit and implement DICOM's Supplement 132, part of the standard since 2008, which would add surfaces and volumes meshes (2 and 3 manifolds) storage capacity to GDCM /ITK. This would add support for surfaces and volume (2 and 3 manifolds in n dimensional space, see supplemental material annex).<br />
We suggest 2 different options. The first option would allow for storage of itk::QuadEdgeMesh as a DICOM file. The second options would allow for storage of an itk::Mesh as a DICOM file. Of course reading the corresponding structures from a DICOM file would also be provided.<br />
As an illustration, we make a clear distinction in what itk::QuadEdgeMesh handles and what itk::Mesh can handle. Both 2 and 3 manifold objects are handled in the DICOM standard.<br />
We do anticipate a large portion of this task to be validation testing. Since there are no other serialization mechanism available in ITK, we will need to setup an hybrid system with VTK to perform validation on the dataset written (a 3D VTK mesh will be used as input for the tests). For this we would be re-using code from InsightApplications/Auxiliary/vtk/vtk2itk.cxx.<br />
<br />
<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
The objectives of the project week is to share with the community and make a list of persons interested and of corresponding efforts before we start implementing. Typically at the end of the week we would like to have identified existing parts, ongoing effort and have a roadmap available possibly with other groups joining in depending on needs, manpower and expertise.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)<br />
<br />
#ITK Module<br />
#Other: GDCM extension (gdcm is included in ITK)<br />
<br />
==References==<br />
*the official DICOM Standard Proposal [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf here]<br />
<br />
</div></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Project_Week_DICOM_supplement_145&diff=537882010 Project Week DICOM supplement 1452010-06-14T04:15:09Z<p>Agouaillard: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Mathieu Malaterre: CoSMo Software<br />
* Alex. Gouaillard: CoSMo SOftware, A*STAR<br />
* NAMIC: (luis?)<br />
<br />
==Project==<br />
DICOM Supplement 145 provide a way to go over the 32bits limits and allow storing of large images. We propose to implement this specification.<br />
In addition, we would implement DICOM specification for JPEG 2000 Part 2 Multi-component Image Compression. This portion of the standard provides higher<br />
compression ratio for storing multicomponent images. <br />
Finally by implementing DICOM supplement 132, we would provides support for storing of surfaces and 3D volumes, as an addition to the 2D RTSTRUCT.<br />
<br />
<br />
<br />
DICOM currently defines Image IODs by storing the rows and columns as unsigned short<br />
integer. This means that an image can only be at most of size 2^16 * 2^16 pixels.<br />
This is a limitation for Microscopy Images as , for example, typical Whole Slice Images an be 60,000 * 80,000 pixels. Since images are generally stored with 24-bit color<br />
pixels, this means WSI can go up to 15Gb. Confocal Microscopy Images add one additional<br />
dimension, and are today already capable of acquiring 24 channels. They are reported to need up<br />
to petabytes.<br />
For this reason DICOM Supplement 145 defines a way to store images into multiple<br />
DICOM files providing a mean to work around this 32bits limitation of DICOM.<br />
By implementing this Supplement (which is still in Ballot), we would provide to the<br />
ITK community a proof of concept and allow people to start saving larges images using DICOM.<br />
This would allow the re-using of technologies and prevent people from re-inventing the wheel<br />
and start using a new file format to exchange medical image (second system effect). <br />
<br />
<br />
<br />
<br />
Microscopy Images, on top of being larger sometimes by several orders of magnitudes from medical images, are also multi-component. Even though ITK handle multicomponent images per say, by defining the right pixel type, nothing is available today for the storage and compression of images that would have more than 3 channels (RGB). Since 2001, the DICOM standard allows JPEG 2000 compression. GDCM 2.x has supported a portion of the standard by providing an API to allow transfer syntax such as JPEG 2000 Image Compression (1.2.840.10008.1.2.4.90 and 1.2.840.10008.1.2.4.91). However the standard also includes JPEG 2000 Part 2 Multi-component Image Compression (1.2.840.10008.1.2.4.92 and 1.2.840.10008.1.2.4.93). The latter has never made into GDCM / ITK, or any other open source DICOM toolkit, since as quoted from the presentation: “Image Compression Refresher – JPEG 2000 and 3D, David Clunie”: the compression gain was modest (using lossless compression). We see now an opportunity that this compression can make it into GDCM / ITK since microscopy images would perfectly fit into the original design of the compression (ISO/IEC 15444-2:2003 Annex J). This would ease the dissemination of large dataset by reusing standard compression techniques, since this would greatly reduce the size of those file datasets. This will be particularly useful for microscopic images. At the time of writing no other open-source DICOM toolkit offer this compression algorithm. <br />
<br />
<br />
<br />
<br />
From its early design, ITK has always offered some n-dimensional n-manifold (polygonal meshes) support through the itk::Mesh class. However at the time of writing of this proposal, there is still no official way to read or write those meshes from and to a filesystem in ITK. Only an hybrid solution is available in Insight Applications. However it implies a dependency to the entire VTK library which is an overkill most of the time.<br />
Thanks to the work on itk::QuadEdgeMesh some progress have been made toward that goal. The Review directory surrently holds a very simple VTK PolyData reader and writer. However, it only supports legacy vtk files using ASCII encoding. For its defense, this implementation was only made for regression testing and illustration of the filters usage.<br />
We are proposing here to fill this gap in the ITK toolkit and implement DICOM's Supplement 132, part of the standard since 2008, which would add surfaces and volumes meshes (2 and 3 manifolds) storage capacity to GDCM /ITK. This would add support for surfaces and volume (2 and 3 manifolds in n dimensional space, see supplemental material annex).<br />
We suggest 2 different options. The first option would allow for storage of itk::QuadEdgeMesh as a DICOM file. The second options would allow for storage of an itk::Mesh as a DICOM file. Of course reading the corresponding structures from a DICOM file would also be provided.<br />
As an illustration, we make a clear distinction in what itk::QuadEdgeMesh handles and what itk::Mesh can handle. Both 2 and 3 manifold objects are handled in the DICOM standard.<br />
We do anticipate a large portion of this task to be validation testing. Since there are no other serialization mechanism available in ITK, we will need to setup an hybrid system with VTK to perform validation on the dataset written (a 3D VTK mesh will be used as input for the tests). For this we would be re-using code from InsightApplications/Auxiliary/vtk/vtk2itk.cxx.<br />
<br />
<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
The objectives of the project week is to share with the community and make a list of persons interested and of corresponding efforts before we start implementing. Typically at the end of the week we would like to have identified existing parts, ongoing effort and have a roadmap available possibly with other groups joining in depending on needs, manpower and expertise.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
<br />
<br />
<br />
<br />
(see the official DICOM Standard Proposal [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf here] )</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week&diff=537872010 Summer Project Week2010-06-14T04:14:13Z<p>Agouaillard: /* Microscopy Image Analysis */</p>
<hr />
<div>__NOTOC__<br />
<br />
Back to [[Project Events]], [[Events]]<br />
<br />
[[Image:PW-MIT2010.png|300px]]<br />
<br />
<br />
==Background==<br />
<br />
We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. <br />
<br />
Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br />
<br />
The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br />
<br />
This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
== Logistics ==<br />
*'''Dates:''' June 21-25, 2010<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.<br />
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). <br />
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process. <br />
<br />
''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''<br />
''' $189/night/room (plus tax).'''<br />
''' This rate is good only through June 1.'''<br />
<br />
Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290. <br />
<br />
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br />
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]<br />
<br />
==Agenda==<br />
=== Monday, June 21, 2010 === <br />
** noon-1pm lunch <br />
**1pm: Welcome (Ron Kikinis)<br />
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template]) <br />
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)<br />
<br />
=== Tuesday, June 22, 2010 ===<br />
** 8:30am breakfast<br />
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.<br />
**9:45-10:30am 3D Slicer Update (Steve Pieper)<br />
**10:30-11am OpenIGTLink Update (Junichi Tokuda)<br />
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)<br />
** noon lunch <br />
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)<br />
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]<br />
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)<br />
** 5:30pm adjourn for day<br />
<br />
=== Wednesday, June 23, 2010 ===<br />
** 8:30am breakfast<br />
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)<br />
** noon lunch<br />
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]<br />
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)<br />
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanez)<br />
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)<br />
** 5:30pm adjourn for day<br />
<br />
=== Thursday, June 24, 2010 ===<br />
** 8:30am breakfast<br />
<br />
** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]<br />
** noon lunch<br />
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)<br />
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)<br />
** 5:30pm adjourn for day<br />
<br />
=== Friday, June 25, 2010 === <br />
** 8:30am breakfast<br />
** 10am-noon: [[#Projects|Project Progress Updates]]<br />
*** Noon: Lunch boxes and adjourn by 1:30pm.<br />
***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br />
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br />
***Next Project Week [[AHM_2011|in Utah]]<br />
<br />
==Projects==<br />
<br />
<br />
<br />
=== Segmentation ===<br />
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)<br />
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)<br />
*[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)<br />
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)<br />
*[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)<br />
*[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)<br />
*[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)<br />
*[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)<br />
*[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)<br />
<br />
=== Registration ===<br />
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)<br />
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)<br />
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)<br />
*[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)<br />
*[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)<br />
*[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)<br />
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)<br />
<br />
=== IGT ===<br />
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)<br />
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi)<br />
* Liver Ablation (Haiying Liu)<br />
* [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)<br />
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)<br />
* [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)<br />
*[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)<br />
*[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)<br />
<br />
=== Radiotherapy ===<br />
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)<br />
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)<br />
*[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )<br />
<br />
=== Analysis ===<br />
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)<br />
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)<br />
*[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)<br />
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)<br />
<br />
===[[Microscopy Image Analysis]] ===<br />
* [[2010 Project Week DICOM supplement 145 | DICOM supplement 145]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)<br />
* [[ Microscopy extensions for ITK]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )<br />
* [[ Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)<br />
* [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)<br />
* [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)<br />
* [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)<br />
* [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)<br />
* [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)<br />
* [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)<br />
* [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)<br />
* [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)<br />
<br />
=== Shape Analysis ===<br />
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)<br />
* [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)<br />
* [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)<br />
<br />
=== Informatics ===<br />
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)<br />
<br />
=== Diffusion ===<br />
*[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)<br />
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)<br />
*[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)<br />
*[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)<br />
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)<br />
*[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)<br />
<br />
=== NA-MIC Kit Internals ===<br />
*Module Inventory (Steve, Jim)<br />
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)<br />
* [[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)<br />
*[[2010_NAMIC_Project_week:XNATE_Client_For_Slicer|XNAT Enterprise webservices client for Slicer]] (Wendy Plesniak, Mark Anderson)<br />
*[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)<br />
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)<br />
<br />
*[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)<br />
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)<br />
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)<br />
<br />
== Preparation ==<br />
<br />
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br />
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!<br />
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
# People doing Slicer related projects should come to project week with slicer built on your laptop.<br />
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).<br />
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br />
<br />
==Attendee List==<br />
<br />
<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font> <br />
<br />
# Nicole Aucoin , BWH<br />
# Michel Audette , Kitware<br />
# Stephen Aylward , Kitware, Inc<br />
# Alexis Boucharin , UNC Neuro Image Research and Analysis Laboratories<br />
# Sylvain Bouix , BWH<br />
# Michael Bowers , Johns Hopkins University<br />
# Francois Budin , UNC<br />
# Everette Burdette , Acoustic MedSystems, Inc.<br />
# Laurent CHAUVIN , Brigham and Women's Hospital<br />
# Min Chen , Johns Hopkins University<br />
# Jason Crane , UCSF<br />
# Manasi Datar , SCI Institute<br />
# Liya Ding , The Ohio State University<br />
# Ryan Eckbo , BWH<br />
# Ilker Ersoy , University of Missouri Columbia<br />
# Andriy Fedorov , Surgical Planning Lab<br />
# Jean-Christophe Fillion-Robin , Kitware Inc.<br />
# Julien Finet , Kitware Inc<br />
# James Fishbaugh , SCI Institute<br />
# Karl Fritscher , UMIT<br />
# Yi Gao , Gerogia Tech<br />
# Arnaud GELAS , Harvard Medical School<br />
# Chris Gorgolewski , SPL<br />
# alexandre gouaillard , CoSMo Software<br />
# Sylvain Gouttard , SCI Institute<br />
# Kedar Grama, Rensselaer Polytechnic Institute<br />
# Daniel Haehn , University of Pennsylvania<br />
# Adel Hafiane , ENSI-Bourges<br />
# Nathan Hageman , <br />
# Dieter Hahn , University Erlangen<br />
# Michael Halle , BWH/SPL<br />
# Corentin Hamel , UNC Chapel Hill<br />
# Nobuhiko Hata , Brigham and Women's Hospital<br />
# Kathryn Hayes , Brigham and Women's Hospital<br />
# Nicholas Herlambang , AZE, Ltd.<br />
# Leslie Holton , Medtronic Navigation<br />
# Luis Ibanez , KITWARE Inc.<br />
# Jayender Jagadeesan , SPL<br />
# Hans Johnson , University of Iowa<br />
# Tina Kapur , Brigham and Women's Hospital<br />
# Ron Kikinis , Brigham and Women's Hospital<br />
# Minjeong Kim , UNC-Chapel Hill<br />
# Ivan Kolesov , Georgia Institute of Technology<br />
# Garrett Larson , UNC-CH<br />
# Rui Li , MGH<br />
# Curtis Lisle , KnowledgeVis, LLC<br />
# Haiying Liu , Brigham and Women's Hospital<br />
# Yanling Liu , SAIC-Frederick, Inc.<br />
# Bradley Lowekamp , Lockheed Martin<br />
# raghu machiraju , The Ohio State University<br />
# Vincent Magnotta , The University of Iowa<br />
# mathieu malaterre , CoSMo Software<br />
# Daniel Marcus , Washington University<br />
# Katie Mastrogiacomo , Brigham and Women's Hospital<br />
# Joy Matsui , University<br />
# Sean Megason , Harvard Medical School<br />
# Dominik Meier , BWH, Boston MA<br />
# bjoern menze , CSAIL MIT<br />
# Mikhail Milchenko , WUSTL<br />
# James Miller , GE Research<br />
# Kishore Mosaliganti , Harvard Medical School<br />
# Marc Niethammer , UNC Chapel Hill<br />
# Isaiah Norton , BWH Neurosurgery<br />
# Raghav Padmanabhan , RPI<br />
# Kannappan Palaniappan , university of Missouri<br />
# Beatriz Paniagua , University of North Caolina at Chapel Hill<br />
# Xenophon Papademetris , Yale University<br />
# David Partyka , Kitware Inc<br />
# Pratik Patel , <br />
# Sudhir Pathak , Univeristy Of Pittsburgh<br />
# Marta Peroni , Politecnico di Milano<br />
# Antonin Perrot-Audet , Harvard Medical School<br />
# Steve Pieper , Isomics, Inc.<br />
# Wendy Plesniak , BWH<br />
# Kilian Pohl , IBM<br />
# Sonia Pujol , Brigham and Women's Hospital<br />
# Nicolas Rannou , Harvard Medical School<br />
# Tammy Riklin Raviv , MIT, CSAIL<br />
# Marco Ruiz , UCSD<br />
# William Schroeder , Kitware<br />
# Mark Scully , The Mind Research Network<br />
# Greg Sharp , MGH<br />
# Yundi Shi , UNC Chapel Hill<br />
# Nadya Shusharina , MGH<br />
# Shantanu Singh , The Ohio State University<br />
# Gareth Smith , Wolfson Medical Imaging Centre (WMIC)<br />
# Lydie Souhait , Harvard Medical School<br />
# Dominik Spinczyk , Silesian University of Technology<br />
# Padmapriya Srinivasan , <br />
# Xiaodong Tao , GE Research<br />
# Junichi Tokuda , Brigham and Women's Hospital<br />
# Tamas Ungi , Queen's University<br />
# Clement Vachet , UNC Chapel Hill<br />
# Gopalkrishna Veni , SCI Institute<br />
# Demian Wassermann , SPL/LMI/PNL<br />
# Adam Weinrich , Nokia<br />
# Sandy Wells , BWH<br />
# Guorong Wu , University of North Carolina at Chapel Hill<br />
# Alexander Yarmarkovich , ISOMICS<br />
# Alexander Zaitsev , Brigham and Womens Hospital</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week&diff=537862010 Summer Project Week2010-06-14T04:13:35Z<p>Agouaillard: /* Microscopy Image Analysis */</p>
<hr />
<div>__NOTOC__<br />
<br />
Back to [[Project Events]], [[Events]]<br />
<br />
[[Image:PW-MIT2010.png|300px]]<br />
<br />
<br />
==Background==<br />
<br />
We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. <br />
<br />
Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br />
<br />
The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br />
<br />
This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
== Logistics ==<br />
*'''Dates:''' June 21-25, 2010<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.<br />
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). <br />
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process. <br />
<br />
''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''<br />
''' $189/night/room (plus tax).'''<br />
''' This rate is good only through June 1.'''<br />
<br />
Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290. <br />
<br />
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br />
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]<br />
<br />
==Agenda==<br />
=== Monday, June 21, 2010 === <br />
** noon-1pm lunch <br />
**1pm: Welcome (Ron Kikinis)<br />
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template]) <br />
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)<br />
<br />
=== Tuesday, June 22, 2010 ===<br />
** 8:30am breakfast<br />
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.<br />
**9:45-10:30am 3D Slicer Update (Steve Pieper)<br />
**10:30-11am OpenIGTLink Update (Junichi Tokuda)<br />
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)<br />
** noon lunch <br />
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)<br />
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]<br />
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)<br />
** 5:30pm adjourn for day<br />
<br />
=== Wednesday, June 23, 2010 ===<br />
** 8:30am breakfast<br />
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)<br />
** noon lunch<br />
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]<br />
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)<br />
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanez)<br />
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)<br />
** 5:30pm adjourn for day<br />
<br />
=== Thursday, June 24, 2010 ===<br />
** 8:30am breakfast<br />
<br />
** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]<br />
** noon lunch<br />
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)<br />
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)<br />
** 5:30pm adjourn for day<br />
<br />
=== Friday, June 25, 2010 === <br />
** 8:30am breakfast<br />
** 10am-noon: [[#Projects|Project Progress Updates]]<br />
*** Noon: Lunch boxes and adjourn by 1:30pm.<br />
***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br />
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br />
***Next Project Week [[AHM_2011|in Utah]]<br />
<br />
==Projects==<br />
<br />
<br />
<br />
=== Segmentation ===<br />
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)<br />
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)<br />
*[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)<br />
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)<br />
*[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)<br />
*[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)<br />
*[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)<br />
*[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)<br />
*[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)<br />
<br />
=== Registration ===<br />
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)<br />
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)<br />
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)<br />
*[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)<br />
*[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)<br />
*[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)<br />
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)<br />
<br />
=== IGT ===<br />
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)<br />
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi)<br />
* Liver Ablation (Haiying Liu)<br />
* [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)<br />
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)<br />
* [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)<br />
*[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)<br />
*[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)<br />
<br />
=== Radiotherapy ===<br />
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)<br />
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)<br />
*[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )<br />
<br />
=== Analysis ===<br />
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)<br />
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)<br />
*[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)<br />
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)<br />
<br />
===[[Microscopy Image Analysis]] ===<br />
* [[2010 Project Week DICOM supplement 145 | DICOM supplement 145]] (see [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf here]: Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)<br />
* [[ Microscopy extensions for ITK]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )<br />
* [[ Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)<br />
* [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)<br />
* [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)<br />
* [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)<br />
* [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)<br />
* [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)<br />
* [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)<br />
* [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)<br />
* [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)<br />
<br />
=== Shape Analysis ===<br />
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)<br />
* [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)<br />
* [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)<br />
<br />
=== Informatics ===<br />
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)<br />
<br />
=== Diffusion ===<br />
*[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)<br />
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)<br />
*[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)<br />
*[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)<br />
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)<br />
*[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)<br />
<br />
=== NA-MIC Kit Internals ===<br />
*Module Inventory (Steve, Jim)<br />
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)<br />
* [[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)<br />
*[[2010_NAMIC_Project_week:XNATE_Client_For_Slicer|XNAT Enterprise webservices client for Slicer]] (Wendy Plesniak, Mark Anderson)<br />
*[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)<br />
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)<br />
<br />
*[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)<br />
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)<br />
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)<br />
<br />
== Preparation ==<br />
<br />
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br />
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!<br />
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
# People doing Slicer related projects should come to project week with slicer built on your laptop.<br />
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).<br />
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br />
<br />
==Attendee List==<br />
<br />
<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font> <br />
<br />
# Nicole Aucoin , BWH<br />
# Michel Audette , Kitware<br />
# Stephen Aylward , Kitware, Inc<br />
# Alexis Boucharin , UNC Neuro Image Research and Analysis Laboratories<br />
# Sylvain Bouix , BWH<br />
# Michael Bowers , Johns Hopkins University<br />
# Francois Budin , UNC<br />
# Everette Burdette , Acoustic MedSystems, Inc.<br />
# Laurent CHAUVIN , Brigham and Women's Hospital<br />
# Min Chen , Johns Hopkins University<br />
# Jason Crane , UCSF<br />
# Manasi Datar , SCI Institute<br />
# Liya Ding , The Ohio State University<br />
# Ryan Eckbo , BWH<br />
# Ilker Ersoy , University of Missouri Columbia<br />
# Andriy Fedorov , Surgical Planning Lab<br />
# Jean-Christophe Fillion-Robin , Kitware Inc.<br />
# Julien Finet , Kitware Inc<br />
# James Fishbaugh , SCI Institute<br />
# Karl Fritscher , UMIT<br />
# Yi Gao , Gerogia Tech<br />
# Arnaud GELAS , Harvard Medical School<br />
# Chris Gorgolewski , SPL<br />
# alexandre gouaillard , CoSMo Software<br />
# Sylvain Gouttard , SCI Institute<br />
# Kedar Grama, Rensselaer Polytechnic Institute<br />
# Daniel Haehn , University of Pennsylvania<br />
# Adel Hafiane , ENSI-Bourges<br />
# Nathan Hageman , <br />
# Dieter Hahn , University Erlangen<br />
# Michael Halle , BWH/SPL<br />
# Corentin Hamel , UNC Chapel Hill<br />
# Nobuhiko Hata , Brigham and Women's Hospital<br />
# Kathryn Hayes , Brigham and Women's Hospital<br />
# Nicholas Herlambang , AZE, Ltd.<br />
# Leslie Holton , Medtronic Navigation<br />
# Luis Ibanez , KITWARE Inc.<br />
# Jayender Jagadeesan , SPL<br />
# Hans Johnson , University of Iowa<br />
# Tina Kapur , Brigham and Women's Hospital<br />
# Ron Kikinis , Brigham and Women's Hospital<br />
# Minjeong Kim , UNC-Chapel Hill<br />
# Ivan Kolesov , Georgia Institute of Technology<br />
# Garrett Larson , UNC-CH<br />
# Rui Li , MGH<br />
# Curtis Lisle , KnowledgeVis, LLC<br />
# Haiying Liu , Brigham and Women's Hospital<br />
# Yanling Liu , SAIC-Frederick, Inc.<br />
# Bradley Lowekamp , Lockheed Martin<br />
# raghu machiraju , The Ohio State University<br />
# Vincent Magnotta , The University of Iowa<br />
# mathieu malaterre , CoSMo Software<br />
# Daniel Marcus , Washington University<br />
# Katie Mastrogiacomo , Brigham and Women's Hospital<br />
# Joy Matsui , University<br />
# Sean Megason , Harvard Medical School<br />
# Dominik Meier , BWH, Boston MA<br />
# bjoern menze , CSAIL MIT<br />
# Mikhail Milchenko , WUSTL<br />
# James Miller , GE Research<br />
# Kishore Mosaliganti , Harvard Medical School<br />
# Marc Niethammer , UNC Chapel Hill<br />
# Isaiah Norton , BWH Neurosurgery<br />
# Raghav Padmanabhan , RPI<br />
# Kannappan Palaniappan , university of Missouri<br />
# Beatriz Paniagua , University of North Caolina at Chapel Hill<br />
# Xenophon Papademetris , Yale University<br />
# David Partyka , Kitware Inc<br />
# Pratik Patel , <br />
# Sudhir Pathak , Univeristy Of Pittsburgh<br />
# Marta Peroni , Politecnico di Milano<br />
# Antonin Perrot-Audet , Harvard Medical School<br />
# Steve Pieper , Isomics, Inc.<br />
# Wendy Plesniak , BWH<br />
# Kilian Pohl , IBM<br />
# Sonia Pujol , Brigham and Women's Hospital<br />
# Nicolas Rannou , Harvard Medical School<br />
# Tammy Riklin Raviv , MIT, CSAIL<br />
# Marco Ruiz , UCSD<br />
# William Schroeder , Kitware<br />
# Mark Scully , The Mind Research Network<br />
# Greg Sharp , MGH<br />
# Yundi Shi , UNC Chapel Hill<br />
# Nadya Shusharina , MGH<br />
# Shantanu Singh , The Ohio State University<br />
# Gareth Smith , Wolfson Medical Imaging Centre (WMIC)<br />
# Lydie Souhait , Harvard Medical School<br />
# Dominik Spinczyk , Silesian University of Technology<br />
# Padmapriya Srinivasan , <br />
# Xiaodong Tao , GE Research<br />
# Junichi Tokuda , Brigham and Women's Hospital<br />
# Tamas Ungi , Queen's University<br />
# Clement Vachet , UNC Chapel Hill<br />
# Gopalkrishna Veni , SCI Institute<br />
# Demian Wassermann , SPL/LMI/PNL<br />
# Adam Weinrich , Nokia<br />
# Sandy Wells , BWH<br />
# Guorong Wu , University of North Carolina at Chapel Hill<br />
# Alexander Yarmarkovich , ISOMICS<br />
# Alexander Zaitsev , Brigham and Womens Hospital</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Project_Week_DICOM_supplement_145&diff=537842010 Project Week DICOM supplement 1452010-06-14T04:11:06Z<p>Agouaillard: moved DICOM supplement 145 to 2010 Project Week DICOM supplement 145:&#32;compliance with name style</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Mathieu Malaterre: CoSMo Software<br />
* Alex. Gouaillard: CoSMo SOftware, A*STAR<br />
* NAMIC: (luis?)<br />
<br />
==Project==<br />
DICOM Supplement 145 provide a way to go over the 32bits limits and allow storing of large images. We propose to implement this specification.<br />
In addition, we would implement DICOM specification for JPEG 2000 Part 2 Multi-component Image Compression. This portion of the standard provides higher<br />
compression ratio for storing multicomponent images. <br />
Finally by implementing DICOM supplement 132, we would provides support for storing of surfaces and 3D volumes, as an addition to the 2D RTSTRUCT.<br />
<br />
<br />
<br />
DICOM currently defines Image IODs by storing the rows and columns as unsigned short<br />
integer. This means that an image can only be at most of size 2^16 * 2^16 pixels.<br />
This is a limitation for Microscopy Images as , for example, typical Whole Slice Images an be 60,000 * 80,000 pixels. Since images are generally stored with 24-bit color<br />
pixels, this means WSI can go up to 15Gb. Confocal Microscopy Images add one additional<br />
dimension, and are today already capable of acquiring 24 channels. They are reported to need up<br />
to petabytes.<br />
For this reason DICOM Supplement 145 defines a way to store images into multiple<br />
DICOM files providing a mean to work around this 32bits limitation of DICOM.<br />
By implementing this Supplement (which is still in Ballot), we would provide to the<br />
ITK community a proof of concept and allow people to start saving larges images using DICOM.<br />
This would allow the re-using of technologies and prevent people from re-inventing the wheel<br />
and start using a new file format to exchange medical image (second system effect). <br />
<br />
<br />
<br />
<br />
Microscopy Images, on top of being larger sometimes by several orders of magnitudes from medical images, are also multi-component. Even though ITK handle multicomponent images per say, by defining the right pixel type, nothing is available today for the storage and compression of images that would have more than 3 channels (RGB). Since 2001, the DICOM standard allows JPEG 2000 compression. GDCM 2.x has supported a portion of the standard by providing an API to allow transfer syntax such as JPEG 2000 Image Compression (1.2.840.10008.1.2.4.90 and 1.2.840.10008.1.2.4.91). However the standard also includes JPEG 2000 Part 2 Multi-component Image Compression (1.2.840.10008.1.2.4.92 and 1.2.840.10008.1.2.4.93). The latter has never made into GDCM / ITK, or any other open source DICOM toolkit, since as quoted from the presentation: “Image Compression Refresher – JPEG 2000 and 3D, David Clunie”: the compression gain was modest (using lossless compression). We see now an opportunity that this compression can make it into GDCM / ITK since microscopy images would perfectly fit into the original design of the compression (ISO/IEC 15444-2:2003 Annex J). This would ease the dissemination of large dataset by reusing standard compression techniques, since this would greatly reduce the size of those file datasets. This will be particularly useful for microscopic images. At the time of writing no other open-source DICOM toolkit offer this compression algorithm. <br />
<br />
<br />
<br />
<br />
From its early design, ITK has always offered some n-dimensional n-manifold (polygonal meshes) support through the itk::Mesh class. However at the time of writing of this proposal, there is still no official way to read or write those meshes from and to a filesystem in ITK. Only an hybrid solution is available in Insight Applications. However it implies a dependency to the entire VTK library which is an overkill most of the time.<br />
Thanks to the work on itk::QuadEdgeMesh some progress have been made toward that goal. The Review directory surrently holds a very simple VTK PolyData reader and writer. However, it only supports legacy vtk files using ASCII encoding. For its defense, this implementation was only made for regression testing and illustration of the filters usage.<br />
We are proposing here to fill this gap in the ITK toolkit and implement DICOM's Supplement 132, part of the standard since 2008, which would add surfaces and volumes meshes (2 and 3 manifolds) storage capacity to GDCM /ITK. This would add support for surfaces and volume (2 and 3 manifolds in n dimensional space, see supplemental material annex).<br />
We suggest 2 different options. The first option would allow for storage of itk::QuadEdgeMesh as a DICOM file. The second options would allow for storage of an itk::Mesh as a DICOM file. Of course reading the corresponding structures from a DICOM file would also be provided.<br />
As an illustration, we make a clear distinction in what itk::QuadEdgeMesh handles and what itk::Mesh can handle. Both 2 and 3 manifold objects are handled in the DICOM standard.<br />
We do anticipate a large portion of this task to be validation testing. Since there are no other serialization mechanism available in ITK, we will need to setup an hybrid system with VTK to perform validation on the dataset written (a 3D VTK mesh will be used as input for the tests). For this we would be re-using code from InsightApplications/Auxiliary/vtk/vtk2itk.cxx.<br />
<br />
<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
The objectives of the project week is to share with the community and make a list of persons interested and of corresponding efforts before we start implementing. Typically at the end of the week we would like to have identified existing parts, ongoing effort and have a roadmap available possibly with other groups joining in depending on needs, manpower and expertise.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=DICOM_supplement_145&diff=53785DICOM supplement 1452010-06-14T04:11:06Z<p>Agouaillard: moved DICOM supplement 145 to 2010 Project Week DICOM supplement 145:&#32;compliance with name style</p>
<hr />
<div>#REDIRECT [[2010 Project Week DICOM supplement 145]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Project_Week_DICOM_supplement_145&diff=537832010 Project Week DICOM supplement 1452010-06-14T04:06:36Z<p>Agouaillard: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Mathieu Malaterre: CoSMo Software<br />
* Alex. Gouaillard: CoSMo SOftware, A*STAR<br />
* NAMIC: (luis?)<br />
<br />
==Project==<br />
DICOM Supplement 145 provide a way to go over the 32bits limits and allow storing of large images. We propose to implement this specification.<br />
In addition, we would implement DICOM specification for JPEG 2000 Part 2 Multi-component Image Compression. This portion of the standard provides higher<br />
compression ratio for storing multicomponent images. <br />
Finally by implementing DICOM supplement 132, we would provides support for storing of surfaces and 3D volumes, as an addition to the 2D RTSTRUCT.<br />
<br />
<br />
<br />
DICOM currently defines Image IODs by storing the rows and columns as unsigned short<br />
integer. This means that an image can only be at most of size 2^16 * 2^16 pixels.<br />
This is a limitation for Microscopy Images as , for example, typical Whole Slice Images an be 60,000 * 80,000 pixels. Since images are generally stored with 24-bit color<br />
pixels, this means WSI can go up to 15Gb. Confocal Microscopy Images add one additional<br />
dimension, and are today already capable of acquiring 24 channels. They are reported to need up<br />
to petabytes.<br />
For this reason DICOM Supplement 145 defines a way to store images into multiple<br />
DICOM files providing a mean to work around this 32bits limitation of DICOM.<br />
By implementing this Supplement (which is still in Ballot), we would provide to the<br />
ITK community a proof of concept and allow people to start saving larges images using DICOM.<br />
This would allow the re-using of technologies and prevent people from re-inventing the wheel<br />
and start using a new file format to exchange medical image (second system effect). <br />
<br />
<br />
<br />
<br />
Microscopy Images, on top of being larger sometimes by several orders of magnitudes from medical images, are also multi-component. Even though ITK handle multicomponent images per say, by defining the right pixel type, nothing is available today for the storage and compression of images that would have more than 3 channels (RGB). Since 2001, the DICOM standard allows JPEG 2000 compression. GDCM 2.x has supported a portion of the standard by providing an API to allow transfer syntax such as JPEG 2000 Image Compression (1.2.840.10008.1.2.4.90 and 1.2.840.10008.1.2.4.91). However the standard also includes JPEG 2000 Part 2 Multi-component Image Compression (1.2.840.10008.1.2.4.92 and 1.2.840.10008.1.2.4.93). The latter has never made into GDCM / ITK, or any other open source DICOM toolkit, since as quoted from the presentation: “Image Compression Refresher – JPEG 2000 and 3D, David Clunie”: the compression gain was modest (using lossless compression). We see now an opportunity that this compression can make it into GDCM / ITK since microscopy images would perfectly fit into the original design of the compression (ISO/IEC 15444-2:2003 Annex J). This would ease the dissemination of large dataset by reusing standard compression techniques, since this would greatly reduce the size of those file datasets. This will be particularly useful for microscopic images. At the time of writing no other open-source DICOM toolkit offer this compression algorithm. <br />
<br />
<br />
<br />
<br />
From its early design, ITK has always offered some n-dimensional n-manifold (polygonal meshes) support through the itk::Mesh class. However at the time of writing of this proposal, there is still no official way to read or write those meshes from and to a filesystem in ITK. Only an hybrid solution is available in Insight Applications. However it implies a dependency to the entire VTK library which is an overkill most of the time.<br />
Thanks to the work on itk::QuadEdgeMesh some progress have been made toward that goal. The Review directory surrently holds a very simple VTK PolyData reader and writer. However, it only supports legacy vtk files using ASCII encoding. For its defense, this implementation was only made for regression testing and illustration of the filters usage.<br />
We are proposing here to fill this gap in the ITK toolkit and implement DICOM's Supplement 132, part of the standard since 2008, which would add surfaces and volumes meshes (2 and 3 manifolds) storage capacity to GDCM /ITK. This would add support for surfaces and volume (2 and 3 manifolds in n dimensional space, see supplemental material annex).<br />
We suggest 2 different options. The first option would allow for storage of itk::QuadEdgeMesh as a DICOM file. The second options would allow for storage of an itk::Mesh as a DICOM file. Of course reading the corresponding structures from a DICOM file would also be provided.<br />
As an illustration, we make a clear distinction in what itk::QuadEdgeMesh handles and what itk::Mesh can handle. Both 2 and 3 manifold objects are handled in the DICOM standard.<br />
We do anticipate a large portion of this task to be validation testing. Since there are no other serialization mechanism available in ITK, we will need to setup an hybrid system with VTK to perform validation on the dataset written (a 3D VTK mesh will be used as input for the tests). For this we would be re-using code from InsightApplications/Auxiliary/vtk/vtk2itk.cxx.<br />
<br />
<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
The objectives of the project week is to share with the community and make a list of persons interested and of corresponding efforts before we start implementing. Typically at the end of the week we would like to have identified existing parts, ongoing effort and have a roadmap available possibly with other groups joining in depending on needs, manpower and expertise.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Project_Week_DICOM_supplement_145&diff=537822010 Project Week DICOM supplement 1452010-06-14T04:05:56Z<p>Agouaillard: /* Project */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Mathieu Malaterre: CoSMo Software<br />
* Alex. Gouaillard: CoSMo SOftware, A*STAR<br />
<br />
==Project==<br />
DICOM Supplement 145 provide a way to go over the 32bits limits and allow storing of large images. We propose to implement this specification.<br />
In addition, we would implement DICOM specification for JPEG 2000 Part 2 Multi-component Image Compression. This portion of the standard provides higher<br />
compression ratio for storing multicomponent images. <br />
Finally by implementing DICOM supplement 132, we would provides support for storing of surfaces and 3D volumes, as an addition to the 2D RTSTRUCT.<br />
<br />
<br />
<br />
DICOM currently defines Image IODs by storing the rows and columns as unsigned short<br />
integer. This means that an image can only be at most of size 2^16 * 2^16 pixels.<br />
This is a limitation for Microscopy Images as , for example, typical Whole Slice Images an be 60,000 * 80,000 pixels. Since images are generally stored with 24-bit color<br />
pixels, this means WSI can go up to 15Gb. Confocal Microscopy Images add one additional<br />
dimension, and are today already capable of acquiring 24 channels. They are reported to need up<br />
to petabytes.<br />
For this reason DICOM Supplement 145 defines a way to store images into multiple<br />
DICOM files providing a mean to work around this 32bits limitation of DICOM.<br />
By implementing this Supplement (which is still in Ballot), we would provide to the<br />
ITK community a proof of concept and allow people to start saving larges images using DICOM.<br />
This would allow the re-using of technologies and prevent people from re-inventing the wheel<br />
and start using a new file format to exchange medical image (second system effect). <br />
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Microscopy Images, on top of being larger sometimes by several orders of magnitudes from medical images, are also multi-component. Even though ITK handle multicomponent images per say, by defining the right pixel type, nothing is available today for the storage and compression of images that would have more than 3 channels (RGB). Since 2001, the DICOM standard allows JPEG 2000 compression. GDCM 2.x has supported a portion of the standard by providing an API to allow transfer syntax such as JPEG 2000 Image Compression (1.2.840.10008.1.2.4.90 and 1.2.840.10008.1.2.4.91). However the standard also includes JPEG 2000 Part 2 Multi-component Image Compression (1.2.840.10008.1.2.4.92 and 1.2.840.10008.1.2.4.93). The latter has never made into GDCM / ITK, or any other open source DICOM toolkit, since as quoted from the presentation: “Image Compression Refresher – JPEG 2000 and 3D, David Clunie”: the compression gain was modest (using lossless compression). We see now an opportunity that this compression can make it into GDCM / ITK since microscopy images would perfectly fit into the original design of the compression (ISO/IEC 15444-2:2003 Annex J). This would ease the dissemination of large dataset by reusing standard compression techniques, since this would greatly reduce the size of those file datasets. This will be particularly useful for microscopic images. At the time of writing no other open-source DICOM toolkit offer this compression algorithm. <br />
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From its early design, ITK has always offered some n-dimensional n-manifold (polygonal meshes) support through the itk::Mesh class. However at the time of writing of this proposal, there is still no official way to read or write those meshes from and to a filesystem in ITK. Only an hybrid solution is available in Insight Applications. However it implies a dependency to the entire VTK library which is an overkill most of the time.<br />
Thanks to the work on itk::QuadEdgeMesh some progress have been made toward that goal. The Review directory surrently holds a very simple VTK PolyData reader and writer. However, it only supports legacy vtk files using ASCII encoding. For its defense, this implementation was only made for regression testing and illustration of the filters usage.<br />
We are proposing here to fill this gap in the ITK toolkit and implement DICOM's Supplement 132, part of the standard since 2008, which would add surfaces and volumes meshes (2 and 3 manifolds) storage capacity to GDCM /ITK. This would add support for surfaces and volume (2 and 3 manifolds in n dimensional space, see supplemental material annex).<br />
We suggest 2 different options. The first option would allow for storage of itk::QuadEdgeMesh as a DICOM file. The second options would allow for storage of an itk::Mesh as a DICOM file. Of course reading the corresponding structures from a DICOM file would also be provided.<br />
As an illustration, we make a clear distinction in what itk::QuadEdgeMesh handles and what itk::Mesh can handle. Both 2 and 3 manifold objects are handled in the DICOM standard.<br />
We do anticipate a large portion of this task to be validation testing. Since there are no other serialization mechanism available in ITK, we will need to setup an hybrid system with VTK to perform validation on the dataset written (a 3D VTK mesh will be used as input for the tests). For this we would be re-using code from InsightApplications/Auxiliary/vtk/vtk2itk.cxx.<br />
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<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
The objectives of the project week is to share with the community and make a list of persons interested and of corresponding efforts before we start implementing. Typically at the end of the week we would like to have identified existing parts, ongoing effort and have a roadmap available possibly with other groups joining in depending on needs, manpower and expertise.<br />
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<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Project_Week_DICOM_supplement_145&diff=537812010 Project Week DICOM supplement 1452010-06-14T03:44:04Z<p>Agouaillard: Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Projects List </gallery> ==Key Investigators== * Mathieu Malaterre: CoSMo Software * Alex. Gouaill…'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Mathieu Malaterre: CoSMo Software<br />
* Alex. Gouaillard: CoSMo SOftware, A*STAR<br />
<br />
==Project==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week&diff=537782010 Summer Project Week2010-06-14T03:08:50Z<p>Agouaillard: /* Microscopy Image Analysis */</p>
<hr />
<div>__NOTOC__<br />
<br />
Back to [[Project Events]], [[Events]]<br />
<br />
[[Image:PW-MIT2010.png|300px]]<br />
<br />
<br />
==Background==<br />
<br />
We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. <br />
<br />
Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br />
<br />
The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br />
<br />
This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
== Logistics ==<br />
*'''Dates:''' June 21-25, 2010<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.<br />
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). <br />
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process. <br />
<br />
''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''<br />
''' $189/night/room (plus tax).'''<br />
''' This rate is good only through June 1.'''<br />
<br />
Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290. <br />
<br />
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br />
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]<br />
<br />
==Agenda==<br />
=== Monday, June 21, 2010 === <br />
** noon-1pm lunch <br />
**1pm: Welcome (Ron Kikinis)<br />
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template]) <br />
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)<br />
<br />
=== Tuesday, June 22, 2010 ===<br />
** 8:30am breakfast<br />
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.<br />
**9:45-10:30am 3D Slicer Update (Steve Pieper)<br />
**10:30-11am OpenIGTLink Update (Junichi Tokuda)<br />
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)<br />
** noon lunch <br />
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)<br />
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]<br />
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)<br />
** 5:30pm adjourn for day<br />
<br />
=== Wednesday, June 23, 2010 ===<br />
** 8:30am breakfast<br />
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)<br />
** noon lunch<br />
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]<br />
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)<br />
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanez)<br />
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)<br />
** 5:30pm adjourn for day<br />
<br />
=== Thursday, June 24, 2010 ===<br />
** 8:30am breakfast<br />
<br />
** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]<br />
** noon lunch<br />
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)<br />
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)<br />
** 5:30pm adjourn for day<br />
<br />
=== Friday, June 25, 2010 === <br />
** 8:30am breakfast<br />
** 10am-noon: [[#Projects|Project Progress Updates]]<br />
*** Noon: Lunch boxes and adjourn by 1:30pm.<br />
***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br />
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br />
***Next Project Week [[AHM_2011|in Utah]]<br />
<br />
==Projects==<br />
<br />
<br />
<br />
=== Segmentation ===<br />
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)<br />
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)<br />
*[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)<br />
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)<br />
*[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)<br />
*[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)<br />
*[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)<br />
*[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)<br />
*[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)<br />
<br />
=== Registration ===<br />
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)<br />
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)<br />
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)<br />
*[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)<br />
*[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)<br />
*[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)<br />
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)<br />
<br />
=== IGT ===<br />
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)<br />
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi)<br />
* Liver Ablation (Haiying Liu)<br />
* [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)<br />
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)<br />
* [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)<br />
*[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)<br />
*[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)<br />
<br />
=== Radiotherapy ===<br />
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)<br />
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)<br />
*[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )<br />
<br />
=== Analysis ===<br />
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)<br />
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)<br />
*[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)<br />
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)<br />
<br />
===[[Microscopy Image Analysis]] ===<br />
* [[ DICOM supplement 145]] (see [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf here]: Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)<br />
* [[ Microscopy extensions for ITK]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )<br />
* [[ Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)<br />
* [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)<br />
* [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)<br />
* [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)<br />
* [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)<br />
* [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)<br />
* [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)<br />
* [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)<br />
* [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)<br />
<br />
=== Shape Analysis ===<br />
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)<br />
* [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)<br />
* [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)<br />
<br />
=== Informatics ===<br />
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)<br />
<br />
=== Diffusion ===<br />
*[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)<br />
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)<br />
*[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)<br />
*[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)<br />
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)<br />
*[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)<br />
<br />
=== NA-MIC Kit Internals ===<br />
*Module Inventory (Steve, Jim)<br />
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)<br />
* [[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)<br />
*[[2010_NAMIC_Project_week:XNATE_Client_For_Slicer|XNAT Enterprise webservices client for Slicer]] (Wendy Plesniak, Mark Anderson)<br />
*[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)<br />
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)<br />
<br />
*[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)<br />
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)<br />
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)<br />
<br />
== Preparation ==<br />
<br />
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br />
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!<br />
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
# People doing Slicer related projects should come to project week with slicer built on your laptop.<br />
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).<br />
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br />
<br />
==Attendee List==<br />
<br />
<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font> <br />
<br />
# Nicole Aucoin , BWH<br />
# Michel Audette , Kitware<br />
# Stephen Aylward , Kitware, Inc<br />
# Alexis Boucharin , UNC Neuro Image Research and Analysis Laboratories<br />
# Sylvain Bouix , BWH<br />
# Michael Bowers , Johns Hopkins University<br />
# Francois Budin , UNC<br />
# Everette Burdette , Acoustic MedSystems, Inc.<br />
# Laurent CHAUVIN , Brigham and Women's Hospital<br />
# Min Chen , Johns Hopkins University<br />
# Jason Crane , UCSF<br />
# Manasi Datar , SCI Institute<br />
# Liya Ding , The Ohio State University<br />
# Ryan Eckbo , BWH<br />
# Ilker Ersoy , University of Missouri Columbia<br />
# Andriy Fedorov , Surgical Planning Lab<br />
# Jean-Christophe Fillion-Robin , Kitware Inc.<br />
# Julien Finet , Kitware Inc<br />
# James Fishbaugh , SCI Institute<br />
# Karl Fritscher , UMIT<br />
# Yi Gao , Gerogia Tech<br />
# Arnaud GELAS , Harvard Medical School<br />
# Chris Gorgolewski , SPL<br />
# alexandre gouaillard , CoSMo Software<br />
# Sylvain Gouttard , SCI Institute<br />
# Kedar Grama, Rensselaer Polytechnic Institute<br />
# Daniel Haehn , University of Pennsylvania<br />
# Adel Hafiane , ENSI-Bourges<br />
# Nathan Hageman , <br />
# Dieter Hahn , University Erlangen<br />
# Michael Halle , BWH/SPL<br />
# Corentin Hamel , UNC Chapel Hill<br />
# Nobuhiko Hata , Brigham and Women's Hospital<br />
# Kathryn Hayes , Brigham and Women's Hospital<br />
# Nicholas Herlambang , AZE, Ltd.<br />
# Leslie Holton , Medtronic Navigation<br />
# Luis Ibanez , KITWARE Inc.<br />
# Jayender Jagadeesan , SPL<br />
# Hans Johnson , University of Iowa<br />
# Tina Kapur , Brigham and Women's Hospital<br />
# Ron Kikinis , Brigham and Women's Hospital<br />
# Minjeong Kim , UNC-Chapel Hill<br />
# Ivan Kolesov , Georgia Institute of Technology<br />
# Garrett Larson , UNC-CH<br />
# Rui Li , MGH<br />
# Curtis Lisle , KnowledgeVis, LLC<br />
# Haiying Liu , Brigham and Women's Hospital<br />
# Yanling Liu , SAIC-Frederick, Inc.<br />
# Bradley Lowekamp , Lockheed Martin<br />
# raghu machiraju , The Ohio State University<br />
# Vincent Magnotta , The University of Iowa<br />
# mathieu malaterre , CoSMo Software<br />
# Daniel Marcus , Washington University<br />
# Katie Mastrogiacomo , Brigham and Women's Hospital<br />
# Joy Matsui , University<br />
# Sean Megason , Harvard Medical School<br />
# Dominik Meier , BWH, Boston MA<br />
# bjoern menze , CSAIL MIT<br />
# Mikhail Milchenko , WUSTL<br />
# James Miller , GE Research<br />
# Kishore Mosaliganti , Harvard Medical School<br />
# Marc Niethammer , UNC Chapel Hill<br />
# Isaiah Norton , BWH Neurosurgery<br />
# Raghav Padmanabhan , RPI<br />
# Kannappan Palaniappan , university of Missouri<br />
# Beatriz Paniagua , University of North Caolina at Chapel Hill<br />
# Xenophon Papademetris , Yale University<br />
# David Partyka , Kitware Inc<br />
# Pratik Patel , <br />
# Sudhir Pathak , Univeristy Of Pittsburgh<br />
# Marta Peroni , Politecnico di Milano<br />
# Antonin Perrot-Audet , Harvard Medical School<br />
# Steve Pieper , Isomics, Inc.<br />
# Wendy Plesniak , BWH<br />
# Kilian Pohl , IBM<br />
# Sonia Pujol , Brigham and Women's Hospital<br />
# Nicolas Rannou , Harvard Medical School<br />
# Tammy Riklin Raviv , MIT, CSAIL<br />
# Marco Ruiz , UCSD<br />
# William Schroeder , Kitware<br />
# Mark Scully , The Mind Research Network<br />
# Greg Sharp , MGH<br />
# Yundi Shi , UNC Chapel Hill<br />
# Nadya Shusharina , MGH<br />
# Shantanu Singh , The Ohio State University<br />
# Gareth Smith , Wolfson Medical Imaging Centre (WMIC)<br />
# Lydie Souhait , Harvard Medical School<br />
# Dominik Spinczyk , Silesian University of Technology<br />
# Padmapriya Srinivasan , <br />
# Xiaodong Tao , GE Research<br />
# Junichi Tokuda , Brigham and Women's Hospital<br />
# Tamas Ungi , Queen's University<br />
# Clement Vachet , UNC Chapel Hill<br />
# Gopalkrishna Veni , SCI Institute<br />
# Demian Wassermann , SPL/LMI/PNL<br />
# Adam Weinrich , Nokia<br />
# Sandy Wells , BWH<br />
# Guorong Wu , University of North Carolina at Chapel Hill<br />
# Alexander Yarmarkovich , ISOMICS<br />
# Alexander Zaitsev , Brigham and Womens Hospital</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=Microscopy_Image_Analysis&diff=53777Microscopy Image Analysis2010-06-14T03:01:45Z<p>Agouaillard: /* Participants */</p>
<hr />
<div>= Open Workshop on Microscopy Image Analysis in ITK and VTK =<br />
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK<br />
<br />
== Preparation ==<br />
If you would like to participate in this workshop then please:<br />
* Add your name to the "Participants" section below<br />
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page<br />
* Register for the overall conference from [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here]<br />
* Create a wiki page describing your project following the preparation instructions on the [[2010_Summer_Project_Week#Preparation]] home page and link this to your project listing<br />
<br />
== Background ==<br />
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.<br />
<br />
== Focus ==<br />
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.<br />
<br />
==Format==<br />
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.<br />
<br />
== Schedule ==<br />
* Monday afternoon- 1 slide lightning talk of project planned for the week using your project page<br />
* Wednesday afternoon<br />
** 1:00pm - 2:20pm: Current efforts (20 minute talks per lab). The goal is to describe the user application you are focussed on, your software approach (demos of software are great), and how others can interface with your efforts.<br />
*** 1:00pm: Megason Lab- Dept of Systems Biology, Harvard<br />
**** Sean Megason - Microscopy image analysis for into imaging of embryogenesis<br />
**** Lydie Souhait - Demo of GoFigure<br />
**** Arnaud Gelas - Interfacing with the Megason Lab<br />
*** 1:20pm: Palaniappan Lab- Univ of Missouri<br />
*** 1:40pm: Machiraju Lab- Univ of Ohio<br />
*** 2:00pm: Roysam Lab- Rensselaer Polytechnic Institute<br />
*** 2:20pm: Gouaillard Lab - Singapore Immunology Network / President Cosmo Software<br />
** 2:40pm: Roundtable discussion of standards/interfaces<br />
*** Image file types<br />
*** Input-output interface for segmentation and tracking filters <br />
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type) <br />
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?<br />
*** Common human tasks<br />
**** Manual segmentation and editing of results<br />
**** Visualization of results<br />
** Future directions<br />
* Friday- 1 slide summary of results for the week using your project page<br />
* The rest of the time will be spent coding on projects<br />
<br />
== Projects ==<br />
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page<br />
<br />
== Participants ==<br />
Please add your name to the list if you are interested in participating in this workshop<br />
# Raghu Machiraju, Ohio State University<br />
# Thierry Pecot, Ohio State University<br />
# Shantanu Singh, Ohio State University<br />
# Liya Ding, Ohio State University<br />
# Kannappan Palaniappan, University of Missouri<br />
# Ilker Ersoy, University of Missouri<br />
# Adel Hafiane, ENSI-Bourges, France<br />
# Yousef Al-Kofahi, Rensselaer Polytechnic Institute<br />
# Kedar Grama, Rensselaer Polytechnic Institute<br />
# Raghav Padmanabhan, Rensselaer Polytechnic Institute<br />
# Arnaud Gelas, Harvard Medical School<br />
# Kishore Mosaliganti, Harvard Medical School<br />
# Nicolas Rannou, Harvard Medical School<br />
# Antonin Perrot-Audet, Harvard Medical School<br />
# Lydie Souhait, Harvard Medical School<br />
# Sean Megason, Harvard Medical School<br />
# Luis Ibanez, Kitware<br />
# Andinet Enquobahrie, Kitware<br />
# Mathieu Malaterre, CoSMo<br />
# Alex. Gouaillard. A*STAR / CoSMo<br />
# Sonia Pujol. Brigham and Women's Hospital<br />
# Steve Pieper, Isomics, Inc.</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=Microscopy_Image_Analysis&diff=53776Microscopy Image Analysis2010-06-14T03:00:57Z<p>Agouaillard: /* Schedule */</p>
<hr />
<div>= Open Workshop on Microscopy Image Analysis in ITK and VTK =<br />
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK<br />
<br />
== Preparation ==<br />
If you would like to participate in this workshop then please:<br />
* Add your name to the "Participants" section below<br />
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page<br />
* Register for the overall conference from [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here]<br />
* Create a wiki page describing your project following the preparation instructions on the [[2010_Summer_Project_Week#Preparation]] home page and link this to your project listing<br />
<br />
== Background ==<br />
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.<br />
<br />
== Focus ==<br />
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.<br />
<br />
==Format==<br />
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.<br />
<br />
== Schedule ==<br />
* Monday afternoon- 1 slide lightning talk of project planned for the week using your project page<br />
* Wednesday afternoon<br />
** 1:00pm - 2:20pm: Current efforts (20 minute talks per lab). The goal is to describe the user application you are focussed on, your software approach (demos of software are great), and how others can interface with your efforts.<br />
*** 1:00pm: Megason Lab- Dept of Systems Biology, Harvard<br />
**** Sean Megason - Microscopy image analysis for into imaging of embryogenesis<br />
**** Lydie Souhait - Demo of GoFigure<br />
**** Arnaud Gelas - Interfacing with the Megason Lab<br />
*** 1:20pm: Palaniappan Lab- Univ of Missouri<br />
*** 1:40pm: Machiraju Lab- Univ of Ohio<br />
*** 2:00pm: Roysam Lab- Rensselaer Polytechnic Institute<br />
*** 2:20pm: Gouaillard Lab - Singapore Immunology Network / President Cosmo Software<br />
** 2:40pm: Roundtable discussion of standards/interfaces<br />
*** Image file types<br />
*** Input-output interface for segmentation and tracking filters <br />
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type) <br />
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?<br />
*** Common human tasks<br />
**** Manual segmentation and editing of results<br />
**** Visualization of results<br />
** Future directions<br />
* Friday- 1 slide summary of results for the week using your project page<br />
* The rest of the time will be spent coding on projects<br />
<br />
== Projects ==<br />
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page<br />
<br />
== Participants ==<br />
Please add your name to the list if you are interested in participating in this workshop<br />
# Raghu Machiraju, Ohio State University<br />
# Thierry Pecot, Ohio State University<br />
# Shantanu Singh, Ohio State University<br />
# Liya Ding, Ohio State University<br />
# Kannappan Palaniappan, University of Missouri<br />
# Ilker Ersoy, University of Missouri<br />
# Adel Hafiane, ENSI-Bourges, France<br />
# Yousef Al-Kofahi, Rensselaer Polytechnic Institute<br />
# Kedar Grama, Rensselaer Polytechnic Institute<br />
# Raghav Padmanabhan, Rensselaer Polytechnic Institute<br />
# Arnaud Gelas, Harvard Medical School<br />
# Kishore Mosaliganti, Harvard Medical School<br />
# Nicolas Rannou, Harvard Medical School<br />
# Antonin Perrot-Audet, Harvard Medical School<br />
# Lydie Souhait, Harvard Medical School<br />
# Sean Megason, Harvard Medical School<br />
# Luis Ibanez, Kitware<br />
# Andinet Enquobahrie, Kitware<br />
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments<br />
# Mathieu Malaterre, CoSMo<br />
# Alex. Gouaillard. A*STAR / CoSMo<br />
# Sonia Pujol. Brigham and Women's Hospital<br />
# Steve Pieper, Isomics, Inc.</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=Microscopy_Image_Analysis&diff=51357Microscopy Image Analysis2010-04-12T17:10:24Z<p>Agouaillard: /* Projects */</p>
<hr />
<div>= Open Workshop on Microscopy Image Analysis in ITK and VTK =<br />
The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK<br />
<br />
== Background ==<br />
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.<br />
<br />
== Focus ==<br />
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.<br />
<br />
==Format==<br />
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.<br />
<br />
== Schedule ==<br />
* Monday afternoon- 1 slide lightning talk of project planned for the week<br />
* Wednesday afternoon<br />
** Current efforts (15 minute talks per lab)<br />
** Roundtable discussion of standards/interfaces<br />
*** Image file types<br />
*** Input-output interface for segmentation and tracking filters <br />
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type) <br />
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?<br />
*** Common human tasks<br />
**** Manual segmentation and editing of results<br />
**** Visualization of results<br />
** Future directions<br />
* Friday- 1 slide summary of results for the week<br />
* The rest of the time will be spent coding on projects<br />
<br />
== Projects ==<br />
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects below<br />
* DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard ( Malaterre, Gouaillard )<br />
* Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more ( Laehman, Gouaillard )<br />
* Flow Cytometry ( Gouaillard )<br />
* --<br />
<br />
== Participants ==<br />
Please add your name to the list if you are interested in participating in this workshop<br />
# Raghu Machiraju, Ohio State University<br />
# Kannappan Palaniappan, University of Missouri<br />
# Badri Roysam, Rensselaer Polytechnic Institute<br />
# Arnaud Gelas, Harvard Medical School<br />
# Kishore Mosaliganti, Harvard Medical School<br />
# Nicolas Rannou, Harvard Medical School<br />
# Antonin Perrot-Audet, Harvard Medical School<br />
# Lydie Souhait, Harvard Medical School<br />
# Sean Megason, Harvard Medical School<br />
# Luis Ibanez, Kitware<br />
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments<br />
# Mathieu Maleterre, CoSMo<br />
# Alex. Gouaillard. A*STAR / CoSMo</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=Microscopy_Image_Analysis&diff=51351Microscopy Image Analysis2010-04-12T17:05:16Z<p>Agouaillard: /* Participants */</p>
<hr />
<div>= Open Workshop on Microscopy Image Analysis in ITK and VTK =<br />
The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK<br />
<br />
== Background ==<br />
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.<br />
<br />
== Focus ==<br />
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.<br />
<br />
==Format==<br />
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.<br />
<br />
== Schedule ==<br />
* Monday afternoon- 1 slide lightning talk of project planned for the week<br />
* Wednesday afternoon<br />
** Current efforts (15 minute talks per lab)<br />
** Roundtable discussion of standards/interfaces<br />
*** Image file types<br />
*** Input-output interface for segmentation and tracking filters <br />
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type) <br />
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?<br />
*** Common human tasks<br />
**** Manual segmentation and editing of results<br />
**** Visualization of results<br />
** Future directions<br />
* Friday- 1 slide summary of results for the week<br />
* The rest of the time will be spent coding on projects<br />
<br />
== Projects ==<br />
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects below<br />
* --<br />
* --<br />
<br />
== Participants ==<br />
Please add your name to the list if you are interested in participating in this workshop<br />
# Raghu Machiraju, Ohio State University<br />
# Kannappan Palaniappan, University of Missouri<br />
# Badri Roysam, Rensselaer Polytechnic Institute<br />
# Arnaud Gelas, Harvard Medical School<br />
# Kishore Mosaliganti, Harvard Medical School<br />
# Nicolas Rannou, Harvard Medical School<br />
# Antonin Perrot-Audet, Harvard Medical School<br />
# Lydie Souhait, Harvard Medical School<br />
# Sean Megason, Harvard Medical School<br />
# Luis Ibanez, Kitware<br />
# Gaetan Lehmann, INRA, Platform of Microscopy and Imaging of Micro-Organism, Animals and Ailments<br />
# Mathieu Maleterre, CoSMo<br />
# Alex. Gouaillard. A*STAR / CoSMo</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week&diff=394202009 Summer Project Week2009-06-23T20:34:30Z<p>Agouaillard: /* Wednesday */</p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
<br />
[[Image:PW2009-v3.png|300px]]<br />
<br />
*'''Dates:''' June 22-26, 2009<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
*32-G451 (in Stata)<br />
**Tue, Wed, Thursday 9am to end<br />
*32-D463 (Star conference room in Stata)<br />
**Tuesday all day<br />
**Wednesday 9-11:30, 1:30-end<br />
*32-D451 (in Stata)<br />
** Tues, Wed, Thurs, all day<br />
*38-413 (Lg Conference room inside EECS Headquarters)<br />
**Tues, Wed, Thurs, 9-end<br />
**Fri, 9-1:00<br />
<br />
==Introduction to the FIRST JOINT PROJECT WEEK==<br />
<br />
We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. <br />
<br />
Active preparation begins on Thursday, April 16th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br />
<br />
The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br />
<br />
This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br />
<br />
A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].<br />
<br />
== Agenda==<br />
Breakout Rooms: 32-D451, 38-413<br />
<br />
=== Monday=== <br />
** noon-1pm lunch <br />
**1pm: Welcome (Ron Kikinis)<br />
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template]) <br />
** 3:30-5:30pm Start project work<br />
=== Tuesday ===<br />
** 8:30am breakfast<br />
** 8:30am-9:30am [[2009_Summer_Project_Week_4D_Imaging_discussion| 4D Imaging Meeting]]<br />
**9:30-10am: NA-MIC Kit Overview (Jim Miller)<br />
** 10-10:30am Slicer 3.4 Update (Steve Pieper) ([[media:2009 NA-MIC Project Week Slicer3.4.ppt|Slides]], [[2009_Summer_Project_Week_Extension_Manager|Project Page]])<br />
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata [[Media:2009SummerProgrammingWeekHataIGT.ppt|Slides]], Scott Hoge [ [[Media:2009_NA-MIC_Project_Week_FastImagingLibrary.ppt|slides]] ])<br />
** noon lunch<br />
** 1pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W) (Star D463 Star Conference Room in Stata)<br />
** 2:00pm-3.00pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis) (In Grier)<br />
** 4:00pm: [[2009_Summer_Project_Week_GWE_Setup| GWE End-To-End Live Demo]] (Marco Ruiz)<br />
** 4:30pm [http://www.cimit.org/forum-current.html CIMIT Forum (At BWH / Carl J. and Ruth Shapiro Cardiovascular Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc. ]<br />
** 5:30pm adjourn for day<br />
<br />
=== Wednesday ===<br />
** 8:30am breakfast<br />
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (32-G451) (Luis Ibanez)<br />
** 10am - 11am 32-D451 taken by Megason Lab.<br />
** noon lunch<br />
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (D463 Star conference room) (Alexandre Gouaillard, Arnaud Gelas, Lydie Souhait, Badri Roysam, Curtis Rueden)<br />
** 5:30pm adjourn for day<br />
<br />
=== Thursday===<br />
** 8:30am breakfast<br />
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]<br />
** noon lunch<br />
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (32-G451) (Dan M.)<br />
** 5:30pm adjourn for day<br />
<br />
=== Friday=== <br />
** 8:30am breakfast<br />
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]<br />
*** Noon: Lunch boxes and adjourn by 1:30pm.<br />
***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br />
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br />
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]<br />
<br />
==Projects==<br />
<br />
=== Segmentation ===<br />
<br />
#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation|Lupus Lesion Segmentation]] (Mark Scully MRN)<br />
#[[2009_Summer_Project_Week_WML_SEgmentation|White Matter Lesion segmentation]] (Minjeong Kim UNC)<br />
#[[2009_Summer_Project_Week_Skull_Stripping|Skull Stripping]] (Snehasish Roy JHU)<br />
#[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)<br />
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation|FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)<br />
#[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Set Framework in ITK]] (Arnaud Gelas, Harvard Medical School)<br />
#[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)<br />
#[[Summer2009:The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)<br />
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)<br />
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)<br />
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)<br />
#[[2009 Summer Project Week Quantify VMTK seg error|Quantifying VMTK User Segmentation Error]] (Dave Welch UIowa)<br />
#[[2009_Summer_Project_Week_Project_Segmentation_of_Atrium_wall|Atrium Wall Segmentation]] (Behnood Gholami Georgia Tech)<br />
<br />
=== Registration ===<br />
<br />
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration|Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)<br />
#[[BSpline Registration in Slicer3|BSpline Registration in Slicer3]] (Samuel Gerber Utah)<br />
#[[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)<br />
#[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)<br />
#[[2009_Summer_Project_Week_Slicer3_registration|Slicer 3 registration ]] (Andrew Rausch BWH PNL)<br />
#[[EPI Correction in Slicer3|EPI Correction in Slicer3]] (Ran Tao Utah)<br />
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)<br />
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)<br />
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI)<br />
#[[2009_Summer_Project_Week_HAMMER_Registration|HAMMER Registration]] (Guorong Wu UNC)<br />
#[[2009_Summer_Project_Week_MCMC_Cuda_Registration|Elastic Non-Rigid Registration using MCMC and CUDA]] (Petter Risholm BWH)<br />
#[[2009_Summer_Project_Week_Cardiac_Blood_Pool_Registration|Cardiac Blood Pool Registration]] (Michal Depa MIT)<br />
<br />
=== IGT ===<br />
<br />
#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)<br />
#[[2009_Summer_Project_Week_Prostate_Robotics|Prostate Robotics]] (Junichi Tokuda BWH)<br />
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)<br />
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite]] (Haiying Liu BWH)<br />
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)<br />
#[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]] (Ben Schwartz BWH)<br />
#[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)<br />
#[[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)<br />
#[[Enhanced Neurosuregery navigation]] (Haytham Elhawary, Brigham and Women's Hospital)<br />
#[[GPU accelerated FEM for simulation and segmentation]] (Megumi Nakao, Brigham and Women's Hospital)<br />
#[[Liver EM segmentation]] (Padma Akella, Brigham and Women's Hlspital)<br />
#[[MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement]] (Greg Fischer, WPI)<br />
<br />
=== Radiotherapy ===<br />
<br />
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)<br />
#[[2009_Summer_Project_Week_Adaptive_RT|Adaptive Radiotherapy for Head,Neck, and Thorax]] (Ivan Kolesov GATech)<br />
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](James Balter U Michigan)<br />
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)<br />
#[[2009_Summer_project_week_adaptive_radiation_planning_visualization]](Cal Hisley, Des Moines University/Mercy Des Moines Medical Center)<br />
<br />
=== Analysis ===<br />
<br />
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)<br />
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Linking atlas data with ontologies of brain morphology and function]] (Michael Halle BWH)<br />
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)<br />
#[[2009_Summer_Project_Week_4D_Imaging|4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)<br />
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer|Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)<br />
#[[2009_Summer_Project_Week_Statistical_Toolbox|multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)<br />
<br />
=== Informatics ===<br />
<br />
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI|XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)<br />
#[[2009_Summer_Project_Week_XNATFS|XNAT File System with FUSE]] (Dan Marcus WUSTL)<br />
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)<br />
#[[2009_Summer_Project_Week_GWE_XNAT|GWE-XNAT Integration]] (Marco Ruiz UCSD)<br />
#[[2009_Summer_Project_Week_GWE_Results_Browser|GWE Results Browser Improvements]] (Marco Ruiz UCSD)<br />
#[[Projects:ShapeCorrespondence_UNCOrthoApp|XNAT & Ortho App]] (Beatriz Paniagua UNC)<br />
<br />
=== Diffusion ===<br />
<br />
#[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Sylvain Bouix BWH)<br />
#[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry BWH)<br />
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)<br />
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep|DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)<br />
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom|DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)<br />
#[[2009_Summer_Project_Week_Hageman_FMTractography|Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)<br />
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)<br />
<br />
<br />
<br />
=== Python ===<br />
<br />
#[[Summer2009:Using_ITK_in_python|Using ITK in python]] (Steve Pieper BWH)<br />
#[[Summer2009:Using_cython|Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)<br />
#[[Summer2009:Implementing_parallelism_in_python|Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)<br />
#[[Summer2009:Using_client_server_paradigm_with_python_and_slicer|Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)<br />
<br />
=== Slicer Internals ===<br />
<br />
#[[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)<br />
#[[2009_Summer_Project_Week_Colors_Module|Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)<br />
#[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)<br />
#[[Slicer3 Informatics Workflow Design & XNAT updates|Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)<br />
#[[Slicer3_FlexibleLayouts | Slicer3 Flexible Layouts]] (Wendy Plesniak BWH)<br />
#[[2009_Summer_Project_Week_Extension_Manager|Slicer3 Extension Manager]] (Katie Hayes BWH)<br />
#[[MeshingSummer2009|IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)<br />
<br />
=== Execution Model ===<br />
<br />
#[[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)<br />
#[[Summer2009:Extension of the Command Line XML Syntax/Interface|Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)<br />
<br />
== Preparation ==<br />
<br />
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br />
# Join the kickoff TCON on April 16, 3pm ET.<br />
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br />
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
# People doing Slicer related projects should come to project week with slicer built on your laptop.<br />
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).<br />
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br />
<br />
<br />
<br />
== Logistics ==<br />
*'''Dates:''' June 22-26, 2009<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
*32-D451 (Stata)<br />
** Mon, noon - end<br />
** Tues, Wed, Thurs, all day<br />
*38-413 (Lg Conference room inside EECS Headquarters)<br />
**Mon, noon-end<br />
**Tues, Wed, Thurs, 9-end<br />
**Fri, 9-1:00<br />
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.<br />
*'''Registration Method''' Add your name to the Attendee List section of this page<br />
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.<br />
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br />
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]<br />
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]<br />
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]<br />
<br />
==Attendee List==<br />
<br />
'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''<br />
{|<br />
|-<br />
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{| class="wikitable sortable"<br />
!First<br />
!Last<br />
!Affiliation<br />
|- style=&#34height:50px&#34<br />
|John<br />
|Melonakos<br />
|AccelerEyes (Wed &amp; Thu morning)<br />
|- style=&#34height:50px&#34<br />
|Jack<br />
|Blevins<br />
|Acoustic Med<br />
|- style=&#34height:50px&#34<br />
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|Burdette<br />
|Acoustic Med (Mon-Wed)<br />
|- style=&#34height:50px&#34<br />
|Dana<br />
|Peters<br />
|Beth Israel Deaconess<br />
|- style=&#34height:50px&#34<br />
|Nicole<br />
|Aucoin<br />
|BWH (NAMIC)<br />
|- style=&#34height:50px&#34<br />
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|Danagoulian<br />
|BWH (NCIGT Collaborator)<br />
|- style=&#34height:50px&#34<br />
|Haytham<br />
|Elhawary<br />
|BWH (NCIGT Collaborator)<br />
|- style=&#34height:50px&#34<br />
|Andriy<br />
|Fedorov<br />
|BWH (NAMIC Collaborator)<br />
|- style=&#34height:50px&#34<br />
|Daniel<br />
|Haehn<br />
|BWH (NAC)<br />
|- style=&#34height:50px&#34<br />
|Michael<br />
|Halle<br />
|BWH (NAC)<br />
|- style=&#34height:50px&#34<br />
|Nobuhiko<br />
|Hata<br />
|BWH (NCIGT)<br />
|- style=&#34height:50px&#34<br />
|Katie<br />
|Hayes<br />
|BWH (NAMIC)<br />
|- style=&#34height:50px&#34<br />
|Scott<br />
|Hoge<br />
|BWH (NCIGT)<br />
|- style=&#34height:50px&#34<br />
|Tina<br />
|Kapur<br />
|BWH (NCIGT, NAMIC)<br />
|- style=&#34height:50px&#34<br />
|Ron<br />
|Kikinis<br />
|BWH (NAMIC, NAC, NCIGT)<br />
|- style=&#34height:50px&#34<br />
|Jayender<br />
|Jagadeesan<br />
|BWH (NCIGT Collaborator)<br />
|- style=&#34height:50px&#34<br />
|Haying<br />
|Liu<br />
|BWH (NCIGT)<br />
|- style=&#34height:50px&#34<br />
|Lauren<br />
|O'Donnell<br />
|BWH (NCIGT)<br />
|- style=&#34height:50px&#34<br />
|Wendy<br />
|Plesniak<br />
|BWH (NAC)<br />
|- style=&#34height:50px&#34<br />
|Megumi<br />
|Nakao<br />
|BWH (NAIST)<br />
|- style=&#34height:50px&#34<br />
|Sonia<br />
|Pujol<br />
|BWH (NAMIC)<br />
|- style=&#34height:50px&#34<br />
|Lei<br />
|Qin<br />
|BWH (NCIGT Collaborator)<br />
|- style=&#34height:50px&#34<br />
|Nicolas<br />
|Rannou<br />
|BWH (NAC)<br />
|- style=&#34height:50px&#34<br />
|Petter<br />
|Risholm<br />
|BWH (NCIGT)<br />
|- style=&#34height:50px&#34<br />
|Florin<br />
|Talos<br />
|BWH (NAC)<br />
|- style=&#34height:50px&#34<br />
|Clare<br />
|Tempany<br />
|BWH (NCIGT)<br />
|- style=&#34height:50px&#34<br />
|Junichi<br />
|Tokuda<br />
|BWH (NCIGT)<br />
|- style=&#34height:50px&#34<br />
|Demian<br />
|Wasserman<br />
|BWH (INRIA)<br />
|- style=&#34height:50px&#34<br />
|Carl-Fredrik<br />
|Westin<br />
|BWH (NAC)<br />
|- style=&#34height:50px&#34<br />
|Sandy<br />
|Wells<br />
|BWH (NAC, NCIGT)<br />
|- style=&#34height:50px&#34<br />
|Lilla<br />
|Zollei<br />
|MGH (NAC)<br />
|- style=&#34height:50px&#34<br />
|Padma<br />
|Akella<br />
|BWH (NCIGT)<br />
|- style=&#34height:50px&#34<br />
|Sylvain<br />
|Bouix<br />
|BWH (PNL)<br />
|- style=&#34height:50px&#34<br />
|Julien<br />
|de Siebenthal<br />
|BWH (PNL)<br />
|- style=&#34height:50px&#34<br />
|Marek<br />
|Kubicki<br />
|BWH (NAMIC DBP PNL)<br />
|- style=&#34height:50px&#34<br />
|Juhana<br />
|Frosen<br />
|BWH Tues only<br />
|- style=&#34height:50px&#34<br />
|Sun Woo<br />
|Lee<br />
|BWH (PNL)<br />
|- style=&#34height:50px&#34<br />
|Jimi<br />
|Malcolm<br />
|BWH (PNL)<br />
|- style=&#34height:50px&#34<br />
|Eric<br />
|Melonakos<br />
|BWH (PNL)<br />
|- style=&#34height:50px&#34<br />
|Yogesh<br />
|Rathi<br />
|BWH (PNL)<br />
|- style=&#34height:50px&#34<br />
|Peter<br />
|Savadjiev<br />
|BWH (PNL)<br />
|- style=&#34height:50px&#34<br />
|Doug<br />
|Terry<br />
|BWH (PNL)<br />
|- style=&#34height:50px&#34<br />
|Andrew<br />
|Rausch<br />
|BWH (Mon only)<br />
|- style=&#34height:50px&#34<br />
|Cal<br />
|Hisley<br />
|Des Moines Unive<br />
|- style=&#34height:50px&#34<br />
|Jim<br />
|Miller<br />
|GE<br />
|- style=&#34height:50px&#34<br />
|Xiaodong<br />
|Tao<br />
|GE<br />
|- style=&#34height:50px&#34<br />
|Vandana<br />
|Mohan<br />
|GA Tech<br />
|- style=&#34height:50px&#34<br />
|Yi<br />
|Gao<br />
|GA Tech<br />
|- style=&#34height:50px&#34<br />
|Ivan<br />
|Kolosev<br />
|GA Tech<br />
|- style=&#34height:50px&#34<br />
|Behnood<br />
|Gholami<br />
|GA Tech<br />
|- style=&#34height:50px&#34<br />
|Ziv<br />
|Yaniv<br />
|Georgetown<br />
|- style=&#34height:50px&#34<br />
|Alex<br />
|Gouaillard<br />
|Harvard Systems Biology<br />
|- style=&#34height:50px&#34<br />
|Arnaud<br />
|Gelas<br />
|Harvard Systems Biology<br />
|- style=&#34height:50px&#34<br />
|Sean<br />
|Megason<br />
|Harvard Systems Biology (Wed only)<br />
|- style=&#34height:50px&#34<br />
|Lydie<br />
|Souhait<br />
|Harvard Systems Biology<br />
|- style=&#34height:50px&#34<br />
|Moti<br />
|Freiman<br />
|Hebrew University of Jerusalem<br />
|- style=&#34height:50px&#34<br />
|Amanda<br />
|Peters<br />
|Harvard SEAS<br />
|- style=&#34height:50px&#34<br />
|Maria Francesca<br />
|Spadea<br />
|Italy<br />
|- style=&#34height:50px&#34<br />
|Curtis<br />
|Lisle<br />
|KnowledgeVis<br />
|- style=&#34height:50px&#34<br />
|Steve<br />
|Pieper<br />
|Isomics<br />
|- style=&#34height:50px&#34<br />
|Alex<br />
|Yarmarkovich<br />
|Isomics<br />
|- style=&#34height:50px&#34<br />
|Nathan<br />
|Cho<br />
|JHU<br />
|- style=&#34height:50px&#34<br />
|Bennett<br />
|Landman<br />
|JHU<br />
|- style=&#34height:50px&#34<br />
|Snehashis<br />
|Roy<br />
|JHU<br />
|- style=&#34height:50px&#34<br />
|Sam<br />
|Song<br />
|JHU<br />
|- style=&#34height:50px&#34<br />
|Sebastien<br />
|Barre<br />
|Kitware<br />
|- style=&#34height:50px&#34<br />
|Luis<br />
|Ibanez<br />
|Kitware<br />
|- style=&#34height:50px&#34<br />
|Daniel<br />
|Blezek<br />
|Mayo<br />
|- style=&#34height:50px&#34<br />
|Yong<br />
|Gao<br />
|MGH<br />
|- style=&#34height:50px&#34<br />
|Randy<br />
|Gollub<br />
|MGH<br />
|- style=&#34height:50px&#34<br />
|Rui<br />
|Li<br />
|MGH<br />
|- style=&#34height:50px&#34<br />
|Greg<br />
|Sharp<br />
|MGH<br />
|- style=&#34height:50px&#34<br />
|Robert<br />
|Yaffe<br />
|MGH - Mon<br />
|- style=&#34height:50px&#34<br />
|Sylvain<br />
|Jaume<br />
|MIT<br />
|- style=&#34height:50px&#34<br />
|Bjoern<br />
|Menze<br />
|MIT<br />
|- style=&#34height:50px&#34<br />
|Jeremy<br />
|Bockholt<br />
|MRN (NAMIC Lupus DBP)<br />
|- style=&#34height:50px&#34<br />
|Mark<br />
|Scully<br />
|MRN (NAMIC Lupus DBP) Tue-Th<br />
|- style=&#34height:50px&#34<br />
|Joe<br />
|Stam<br />
|NVIDIA (Wed &amp; Thurs)<br />
|- style=&#34height:50px&#34<br />
|Kimberly<br />
|Powell<br />
|NVIDIA (Wed)<br />
|- style=&#34height:50px&#34<br />
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|Peroni<br />
|Politecnico di Milano<br />
|- style=&#34height:50px&#34<br />
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|Lasso<br />
|Queen's (NAMIC DBP)<br />
|- style=&#34height:50px&#34<br />
|Yanling<br />
|Liu<br />
|SAIC/NCI-Frederick<br />
|- style=&#34height:50px&#34<br />
|Melanie<br />
|Grebe<br />
|Siemens Corporate Research<br />
|- style=&#34height:50px&#34<br />
|Lining<br />
|Yang<br />
|Siemens Corporate Research<br />
|- style=&#34height:50px&#34<br />
|Harish<br />
|Doddi<br />
|Stanford University<br />
|- style=&#34height:50px&#34<br />
|Marco<br />
|Ruiz<br />
|UCSD<br />
|- style=&#34height:50px&#34<br />
|Nathan<br />
|Hageman<br />
|UCLA (Mon-Thurs)<br />
|- style=&#34height:50px&#34<br />
|Hans<br />
|Johnson<br />
|U Iowa<br />
|- style=&#34height:50px&#34<br />
|Vincent<br />
|Magnotta<br />
|U Iowa<br />
|- style=&#34height:50px&#34<br />
|Jeffrey<br />
|Yager<br />
|U Iowa<br />
|- style=&#34height:50px&#34<br />
|Manasi<br />
|Ramachandran<br />
|U Iowa<br />
|- style=&#34height:50px&#34<br />
|Dave<br />
|Welch<br />
|U Iowa<br />
|- style=&#34height:50px&#34<br />
|Andrzej<br />
|Przybyszewski<br />
|UMass Med (Mon)<br />
|- style=&#34height:50px&#34<br />
|James<br />
|Balter<br />
|U Michigan<br />
|- style=&#34height:50px&#34<br />
|Dan<br />
|McShan<br />
|U Michigan<br />
|- style=&#34height:50px&#34<br />
|Zhou<br />
|Shen<br />
|U Michigan<br />
|- style=&#34height:50px&#34<br />
|Beatriz<br />
|Paniagua<br />
|UNC<br />
|- style=&#34height:50px&#34<br />
|Minjeong<br />
|Kim<br />
|UNC<br />
|- style=&#34height:50px&#34<br />
|Zhexing<br />
|Liu<br />
|UNC<br />
|- style=&#34height:50px&#34<br />
|Clement<br />
|Vachet<br />
|UNC (NAMIC DBP)<br />
|- style=&#34height:50px&#34<br />
|Guorong<br />
|Wu<br />
|UNC<br />
|- style=&#34height:50px&#34<br />
|Samuel<br />
|Gerber<br />
|SCI, Utah<br />
|- style=&#34height:50px&#34<br />
|Ran<br />
|Tao<br />
|SCI, Utah<br />
|- style=&#34height:50px&#34<br />
|Marcel<br />
|Prastawa<br />
|SCI, Utah<br />
|- style=&#34height:50px&#34<br />
|Ross<br />
|Whitaker<br />
|SCI, Utah<br />
|- style=&#34height:50px&#34<br />
|Curtis<br />
|Rueden<br />
|UW-Madison<br />
|- style=&#34height:50px&#34<br />
|Dan<br />
|Marcus<br />
|WUSTL<br />
|- style=&#34height:50px&#34<br />
|Misha<br />
|Milchenko<br />
|WUSTL<br />
|- style=&#34height:50px&#34<br />
|Kevin<br />
|Archie<br />
|WUSTL<br />
|- style=&#34height:50px&#34<br />
|Tim<br />
|Olsen<br />
|WUSTL<br />
|- style=&#34height:50px&#34<br />
|Mehdi<br />
|Esteghamatian<br />
|Robarts Research Inst. / Western Ontario<br />
|- style=&#34height:50px&#34<br />
|Diego<br />
|Cantor<br />
|Robarts Research Inst. / Western Ontario<br />
|- style=&#34height:50px&#34<br />
|Danielle<br />
|Pace<br />
|Robarts Research Inst. / Western Ontario<br />
|- style=&#34height:50px&#34<br />
|Vidya<br />
|Rajagopalan<br />
|VA Tech<br />
|- style=&#34height:50px&#34<br />
|Gregory<br />
|Fischer<br />
|WPI<br />
|- style=&#34height:50px&#34<br />
|Dominique<br />
|Belhachemi<br />
|Yale U (Tu &amp; Wed)<br />
|- style=&#34height:50px&#34<br />
|Alark<br />
|Joshi<br />
|Yale U (Tu &amp; Wed)<br />
|- style=&#34height:50px&#34<br />
|Xenios<br />
|Papademetris<br />
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|- style=&#34height:50px&#34<br />
|Dustin<br />
|Scheinost<br />
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|- style=&#34height:50px&#34<br />
|Michelle<br />
|Borkin<br />
|Harvard SEAS (Mon only)<br />
|- style=&#34height:50px&#34<br />
|Renxin<br />
|Chu<br />
|BWH (NCIGT) (Mon, Tue)<br />
|- style=&#34height:50px&#34<br />
|Ben<br />
|Schwartz<br />
|BWH (NCIGT) (Mon, Tue)<br />
|- style=&#34height:50px&#34<br />
|Marianna<br />
|Jakab<br />
|BWH (NCIGT, NAC) (Mon, Tue)<br />
|- style=&#34height:50px&#34<br />
|Viswanath <br />
|Avasarala<br />
|GE (Wed, Thurs)<br />
|- style=&#34height:50px&#34<br />
|Michal<br />
|Depa<br />
|MIT<br />
|- style=&#34height:50px&#34<br />
|}<br />
|}<br />
<br />
<br />
'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''<br />
<br />
The following was used to convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2009_Project_Week_Breakout_Session:_3D%2BT_Microscopy_Cell_Dataset_Segmentation&diff=371652009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation2009-05-09T22:23:24Z<p>Agouaillard: Created page with 'Following the presentations at the NAMIC project week winter 2009 and publications of the corresponding work in the Insight Journal (see below), we are presenting here our latest...'</p>
<hr />
<div>Following the presentations at the NAMIC project week winter 2009 and publications of the corresponding work in the Insight Journal (see below), we are presenting here our latest work on Cell Segmentation in Confocal Microscopy Datasets. Most of the algorithms we will present here are available in [[http://www.vtk.org/Wiki/ITK_Release_Schedule#Release_3.14_Schedule ITK 3.14]] as classes as well as fully integrated in a free, open-source application called [[http://apps.sourceforge.net/trac/gofigure2/timeline GoFigure2]]. <br />
<br />
Because of the size of the datasets (terabytes), the number of cells to process(millions), the intended audience (biologists), and the fact that we cannot foresee what the requirements will be even one year from now, we designed GoFigure to be a layered application with a plug-in mechanism. The layered approach (IO, Processing, GUI) allows for very easy extension of GoFigure. For example, GoFigure right now handles two IO components: File System, and MySQL Database. Before the end of the year, we plan to have an Omero Component, and a component to support Harvard Medical School specific storage cluster. That IO layer mechanism, along with client-server mechanisms has been one of the key in ParaView or Slicer applications. The danger of an integrated application is to tightly integrate a predefine set of service and never being able to extend it. Fortunately, GoFigure implements a plug-in mechanisms based on Qt to allow extension while still taking advantage of better speed and integration than scripting languages allow. Slicer 3 is a good example of how successful such plug in mechanism can be.<br />
<br />
Here is a detailed list of the features *currently* available that will be presented during this session:<br><br />
< Kishore Mosaliganti><br />
* Chan and Vese level set<br />
* Mulltiphase level set<br />
* Coupled level set for non-overlapping objects segmentation (e.g. ... cells)<br />
* Coupling Membrane channel and Nucleus channel for better segmentation<br />
* Specific pre-processing algorithms for nuclei segmentation<br />
* Cells Tracking using level set<br />
<Arnaud Gelas><br />
* Channel Unmixing using PCA<br />
* A new level set framework with 20x speed increase over existing ITK framework<br />
* Vizualization of terabytes datasets<br />
* 2D Manual segmentation<br />
< Alexandre Gouaillard ><br />
* Layered design<br />
* Specific Streaming framework for Multiphase Level Set<br />
* Multifiles Acquisition "Reader" (with support for Zeiss multi time macro naming convention)<br />
* DataBase Support<br />
< lydie Souhait ><br />
* Qt Widgets <br />
* Qt interface of Visualization layer<br />
* Qt DB front end<br />
<br />
Here is a list of features that are available but not mature enough to be transferred to ITK or integrated in GoFigure<br />
* 3D Manual segmentation (PCA, Level set, ...)<br />
* lineage reconstruction and extraction<br />
* plug in mechanism (Qt based, cannot be transferred to ITK)<br />
<br />
<br />
In a true community sharing spirit, our entire development process is open and free. Our svn server, road map and documentation is hosted on sourceforge and fully public. All our source code has been double-checked to be patent-free, and is distributed under the very permissive BSD licence. Finally, whenever possible, we bring our implementation of the features up to the quality level of the ITK toolkit and transfer them to best serve the community.<br />
<br />
[http://www.na-mic.org/Wiki/index.php/AHM2009:Cell_Segmentation] NAMIC winter 2009 - Cell Segmentation Session<br><br />
[http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week:GoFigure] NAMIC winter 2008 - GoFigure Presentation<br><br />
[[2009_Winter_Project_Week_Gofigure_LevelSet|[3]]] NAMIC winter 2009 - ITK level set solution for cell segmentation in microscopy datasets<br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets|[4]]] NAMIC winter 2009 - VTK widgets for manual segmentation and manual validation of segmentation<br><br />
*Mosaliganti, Smith, Gelas, Gouaillard, Megason, "Level Set Segmentation: Active Contours without edge", [[http://hdl.handle.net/1926/1532 Insight Journal]]<br />
*Mosaliganti, Gelas, Gouaillard, Megason, "Microscopy Image Analysis: Blob Segmentation using Geodesic Active Contours", [[http://hdl.handle.net/1926/1531 Insight Journal]]<br />
*Mosaliganti, Smith, Gelas, Gouaillard, Megason, "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes", [[http://hdl.handle.net/10380/3055 Insight Journal]]<br />
*Mosaliganti, Smith, Gelas, Gouaillard, Megason, "level set segmentation using coupled active surfaces", [[http://hdl.handle.net/1926/1533 Insight Journal]]<br />
*Gouaillard , Brown, Bronner-Fraser, Fraser, Megason, "GoFigure and The Digital Fish Project: Open tools and open data for an imaging based approach to system biology", [[http://hdl.handle.net/1926/565 Insight Journal]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=37164MegasonLab2009-05-09T20:58:14Z<p>Agouaillard: /* The Megason Lab */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
<br />
<br />
*Mosaliganti, Smith, Gelas, Gouaillard, Megason, "Level Set Segmentation: Active Contours without edge", [[http://hdl.handle.net/1926/1532 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Surface Meshes Smoothing", [[http://hdl.handle.net/1926/1518 Insight Journal]]<br />
*Mosaliganti, Gelas, Gouaillard, Megason, "Microscopy Image Analysis: Blob Segmentation using Geodesic Active Contours", [[http://hdl.handle.net/1926/1531 Insight Journal]]<br />
*Mosaliganti, Smith, Gelas, Gouaillard, Megason, "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes", [[http://hdl.handle.net/10380/3055 Insight Journal]]<br />
*Mosaliganti, Smith, Gelas, Gouaillard, Megason, "level set segmentation using coupled active surfaces", [[http://hdl.handle.net/1926/1533 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Surface Mesh Discrete Curvature Estimators", [[http://hdl.handle.net/1926/1494 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Surface Mesh Normals Filter", [[http://hdl.handle.net/1926/1495 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Surface Meshes Incremental Decimation Framework", [[http://hdl.handle.net/1926/1488 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Triangular Meshes Delaunay Conforming Filter", [[http://hdl.handle.net/1926/1489 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Mutable Priority Queue Container", [[http://hdl.handle.net/1926/1395 Insight Journal]]<br />
*Gelas, Gouaillard, "Parameterization of discrete surfaces", [[http://hdl.handle.net/1926/1315 Insight Journal]]<br />
*Gouaillard , Brown, Bronner-Fraser, Fraser, Megason, "GoFigure and The Digital Fish Project: Open tools and open data for an imaging based approach to system biology", [[http://hdl.handle.net/1926/565 Insight Journal]]<br />
*Gouaillard, Florez, Boix, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, [[http://hdl.handle.net/1926/306 Insight Journal ]]<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2009_Winter_Project_Week|2009 January: Project Event 8]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti) <br><br />
[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard) <br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas) <br><br />
<br />
<br />
----<br />
[[AHM2009:Cell Segmentation|Cell Segmentation breakout session]] (Alex G, arnaud G, Kishore M)<br />
<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Summer_Project_Week|2008 June: Project Event 7]] ==<br />
This event is scheduled for <br />
<br />
----<br />
<br />
<br />
----<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
<br />
----<br />
<br />
We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
<br />
|-<br />
| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
| |<br />
<br />
== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
<br />
----<br />
<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=37163MegasonLab2009-05-09T20:56:51Z<p>Agouaillard: /* The Megason Lab */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
<br />
<br />
*Mosaliganti, Smith, Gelas, Gouaillard, Megason, "Level Set Segmentation: Active Contours without edge", [[http://hdl.handle.net/1926/1532 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Surface Meshes Smoothing", [[http://hdl.handle.net/10380/3055 Insight Journal]]<br />
*Mosaliganti, Gelas, Gouaillard, Megason, "Microscopy Image Analysis: Blob Segmentation using Geodesic Active Contours", [[http://hdl.handle.net/1926/1531 Insight Journal]]<br />
*Mosaliganti, Smith, Gelas, Gouaillard, Megason, "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes", [[http://hdl.handle.net/10380/3055 Insight Journal]]<br />
*Mosaliganti, Smith, Gelas, Gouaillard, Megason, "level set segmentation using coupled active surfaces", [[http://hdl.handle.net/1926/1533 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Surface Mesh Discrete Curvature Estimators", [[http://hdl.handle.net/1926/1494 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Surface Mesh Normals Filter", [[http://hdl.handle.net/1926/1495 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Surface Meshes Incremental Decimation Framework", [[http://hdl.handle.net/1926/1488 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Triangular Meshes Delaunay Conforming Filter", [[http://hdl.handle.net/1926/1489 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Mutable Priority Queue Container", [[http://hdl.handle.net/1926/1395 Insight Journal]]<br />
*Gelas, Gouaillard, "Parameterization of discrete surfaces", [[http://hdl.handle.net/1926/1315 Insight Journal]]<br />
*Gouaillard , Brown, Bronner-Fraser, Fraser, Megason, "GoFigure and The Digital Fish Project: Open tools and open data for an imaging based approach to system biology", [[http://hdl.handle.net/1926/565 Insight Journal]]<br />
*Gouaillard, Florez, Boix, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, [[http://hdl.handle.net/1926/306 Insight Journal ]]<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2009_Winter_Project_Week|2009 January: Project Event 8]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti) <br><br />
[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard) <br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas) <br><br />
<br />
<br />
----<br />
[[AHM2009:Cell Segmentation|Cell Segmentation breakout session]] (Alex G, arnaud G, Kishore M)<br />
<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Summer_Project_Week|2008 June: Project Event 7]] ==<br />
This event is scheduled for <br />
<br />
----<br />
<br />
<br />
----<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
<br />
----<br />
<br />
We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
<br />
|-<br />
| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
| |<br />
<br />
== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
<br />
----<br />
<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week&diff=371622009 Summer Project Week2009-05-09T20:12:39Z<p>Agouaillard: /* Agenda */</p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
<br />
*'''Dates:''' June 22-26, 2009<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
<br />
<br />
==Introduction to the FIRST JOINT PROJECT WEEK==<br />
<br />
We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. <br />
<br />
Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br />
<br />
The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br />
<br />
This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br />
<br />
A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].<br />
<br />
== Agenda==<br />
* Monday <br />
** noon-1pm lunch <br />
**1pm: Welcome (Ron Kikinis)<br />
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]]) <br />
** 3:30-5:30pm Start project work<br />
* Tuesday <br />
** 8:30am breakfast<br />
**9:30-10am: NA-MIC Kit Overview (Jim Miller)<br />
** 10-10:30am Slicer 3.4 Update (Steve Pieper)<br />
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)<br />
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)<br />
** noon lunch<br />
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]]<br />
** 5:30pm adjourn for day<br />
* Wednesday <br />
** 8:30am breakfast<br />
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)<br />
** noon lunch<br />
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)<br />
** 5:30pm adjourn for day<br />
* Thursday<br />
** 8:30am breakfast<br />
** 9-11pm Tutorial Contest Presentations<br />
** noon lunch<br />
** 2:30pm: Breakout Session: TBD<br />
** 5:30pm adjourn for day<br />
* Friday <br />
** 8:30am breakfast<br />
** 10am-noon: Tutorial Contest Winner Announcement and Project Progress using update [[#Projects|Project Wiki pages]]<br />
*** Noon: Lunch boxes and adjourn by 1:30pm.<br />
***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br />
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br />
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]<br />
<br />
== Projects ==<br />
<br />
The list of projects for this week will go here.<br />
<br />
#Prostate Robotics (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)<br />
#4D Imaging - currently used for Lung Perfusion (Junichi, Dan Blezek?, Steve, Alex G?)<br />
#Liver Ablation in Slicer (Haiying, Georgetown?)<br />
#SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)<br />
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)<br />
#gpu based registration acceleration (James Balter, Greg Sharp, Alark Joshi?, Aditya K., Yogesh Rathi?, Jimi Malcolm, Sandy Wells, Tina Kapur)<br />
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)<br />
#Xnat user interface improvements for NA-MIC (Dan M, Tina, Florin, Ron, Wendy)<br />
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?<br />
#Xnat user clinic - combine with data clinic<br />
#xnat programmer clinic<br />
#Grid Wizard+xnat clinic (Clement)<br />
#?Fluid Mechanincs Module (Nathan Hageman)<br />
#?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)<br />
#Cortical Thickness Pipeline (Clement, Ipek)<br />
#Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)<br />
#Skull Stripping (Xiadong)<br />
<br />
IGT Projects:<br />
#port 4d gated ultrasound code to Slicer - (Danielle)<br />
#integration of stereo video into Slicer (Mehdi)<br />
#multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego, sylvain jaume, nicholas, noby)<br />
#neuroendoscope workflow presentation (sebastien barre)<br />
#slicer integration of mri compatible prostate biopsy robot(sid, queens)<br />
#breakout session on Dynamic Patient Models (James Balter)<br />
#gpu acceleration of 2d-3d registration (james balter, greg sharp, sandy wells, noby hata, terry peters proxy)<br />
<br />
NA-MIC Engineering Projects<br />
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)<br />
# Using ITK in python (Steve, Demian, Jim)<br />
# VTK 3d Widgets in Slicer3 (Nicole, Will/Karthik)<br />
# Update to Slicer3 Colors module (Nicole)<br />
# EM Segmenter (Sylvain, Nicolas)<br />
# Plug-in 3D Viewer based on XIP (Lining)<br />
# IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)<br />
# Informatics workflow Design (Wen, Steve, Dan M, Dan B)<br />
<br />
== Preparation ==<br />
<br />
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br />
# Join the kickoff TCON on April 16, 3pm ET.<br />
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br />
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
<br />
==Attendee List==<br />
If you plan to attend, please add your name here.<br />
<br />
#Ron Kikinis, BWH<br />
#Ferenc Jolesz, BWH<br />
#Clare Tempany, BWH<br />
#Tina Kapur, BWH<br />
#Steve Pieper, Isomics Inc<br />
#Jim Miller, GE Research<br />
#Xiaodong Tao, GE Research<br />
#Bill Lorensen, EAB<br />
#Randy Gollub, MGH<br />
#Nicole Aucoin, BWH<br />
#Dan Marcus, WUSTL<br />
#Junichi Tokuda, BWH<br />
#Alex Gouaillard, Harvard Systems Biology<br />
#Arnaud Gelas, Harvard Systems Biology <br />
#Kishore Mosanliganti, Harvard Systems Biology<br />
#Lydie Souhait, Harvard Systems Biology<br />
#Luis Ibanez, Kitware Inc<br />
#Vincent Magnotta, UIowa<br />
#Hans Johnson, UIowa<br />
#Xenios Papademetris, Yale<br />
#Gregory S. Fischer, WPI (Mon, Tue, Wed)<br />
#Daniel Blezek, Mayo (Tue-Fri)<br />
#Danielle Pace, Robarts Research Institute / UWO<br />
#Clement Vachet, UNC-Chapel Hill<br />
#Dave Welch, UIowa<br />
#Demian Wassermann, Odyssée lab, INRIA, France<br />
#Manasi Ramachandran, UIowa<br />
#Greg Sharp, MGH<br />
#Rui Li, MGH<br />
#Mehdi Esteghamatian, Robarts Research Institute / UWO<br />
#Misha Milchenko, WUSTL<br />
#Kevin Archie, WUSTL<br />
#Tim Olsen, WUSTL<br />
#Wendy Plesniak BWH<br />
#Haiying Liu BWH<br />
#Curtis Lisle, KnowledgeVis / Isomics<br />
#Diego Cantor, Robarts Research Institute / UWO<br />
#Daniel Haehn, BWH<br />
#Nicolas Rannou, BWH<br />
#Sylvain Jaume, MIT<br />
#Alex Yarmarkovich, Isomics<br />
#Marco Ruiz, UCSD<br />
#Andriy Fedorov, BWH<br />
#Harish Doddi, Stanford University<br />
#Saikat Pal, Stanford University<br />
#Scott Hoge, BWH<br />
#Vandana Mohan, Georgia Tech<br />
#Ivan Kolosev, Georgia Tech<br />
#Behnood Gholami, Georgia Tech<br />
#James Balter, U Michigan<br />
#Dan McShan, U Michigan<br />
#Zhou Shen, U Michigan<br />
#Maria Francesca Spadea, Italy<br />
#Lining Yang, Siemens Corporate Research<br />
#Beatriz Paniagua, UNC-Chapel Hill<br />
#Bennett Landman, Johns Hopkins University <br />
#Snehashis Roy, Johns Hopkins University <br />
<br />
== Logistics ==<br />
*'''Dates:''' June 22-26, 2009<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.<br />
*'''Registration Method''' Add your name to the Attendee List section of this page<br />
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.<br />
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br />
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]<br />
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]<br />
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week&diff=361452009 Summer Project Week2009-04-10T15:51:37Z<p>Agouaillard: /* Attendee List */</p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
<br />
*'''Dates:''' June 22-26, 2009<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
<br />
<br />
==Introduction to the FIRST JOINT PROJECT WEEK==<br />
<br />
We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. <br />
<br />
Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br />
<br />
The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br />
<br />
This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br />
<br />
A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].<br />
<br />
== Agenda==<br />
* Monday <br />
** noon-1pm lunch <br />
**1pm: Welcome (Ron Kikinis)<br />
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]]) <br />
** 3:30-5:30pm Start project work<br />
* Tuesday <br />
** 8:30am breakfast<br />
**9:30-10am: NA-MIC Kit Overview (Jim Miller)<br />
** 10-10:30am Slicer 3.4 Update (Steve Pieper)<br />
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)<br />
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)<br />
** noon lunch<br />
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]]<br />
** 5:30pm adjourn for day<br />
* Wednesday <br />
** 8:30am breakfast<br />
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)<br />
** noon lunch<br />
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 4D+T Microscopy Cell Dataset Segmentation]] (Alex G.)<br />
** 5:30pm adjourn for day<br />
* Thursday<br />
** 8:30am breakfast<br />
** 9-11pm Tutorial Contest Presentations<br />
** noon lunch<br />
** 2:30pm: Breakout Session: TBD<br />
** 5:30pm adjourn for day<br />
* Friday <br />
** 8:30am breakfast<br />
** 10am-noon: Tutorial Contest Winner Announcement and Project Progress using update [[#Projects|Project Wiki pages]]<br />
*** Noon: Lunch boxes and adjourn by 1:30pm.<br />
***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br />
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br />
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]<br />
<br />
== Projects ==<br />
<br />
The list of projects for this week will go here.<br />
<br />
== Preparation ==<br />
<br />
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br />
# Join the kickoff TCON on April 16, 3pm ET.<br />
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br />
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
<br />
==Attendee List==<br />
If you plan to attend, please add your name here.<br />
<br />
#Ron Kikinis<br />
#Ferenc Jolesz<br />
#Clare Tempany<br />
#Tina Kapur<br />
#Steve Pieper<br />
#Jim Miller<br />
#Bill Lorensen<br />
#Randy Gollub<br />
#Nicole Aucoin<br />
#Dan Marcus<br />
#Junichi Tokuda<br />
#Alex Gouaillard<br />
#Arnaud Gelas<br />
#Kishore Mosanliganti<br />
#lydie Souhait<br />
<br />
== Logistics ==<br />
*'''Dates:''' June 22-26, 2009<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
*'''Registration Fee:''' TBD (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.<br />
*'''Registration Method''' Add your name to the Attendee List section of this page<br />
*'''Hotel:''' We have a group rate of XXX/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B Please click here to reserve.] This rate is good only through June 1.<br />
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br />
*2008 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]<br />
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]<br />
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2009_Winter_Project_Week_Surface_Processing&diff=359182009 Winter Project Week Surface Processing2009-03-28T19:25:49Z<p>Agouaillard: </p>
<hr />
<div>{|<br />
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]<br />
|<br />
|<br />
|}<br />
<br />
<br />
__NOTOC__<br />
<br />
<br />
===Key Investigators===<br />
* Arnaud Gelas, Harvard Medical School<br />
* Alexandre Gouaillard, Harvard Medical School<br />
* Luis Ibanez<br />
<br />
<div style="margin: 20px;"><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Objective</h1><br />
<br />
* Implement<br />
* Test<br />
* run on examples<br />
* Write corresponding IJ paper<br />
* submit to IJ<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Approach, Plan</h1><br />
* Filters are already implemented<br />
* Code Review with an ITK expert (luis/bill/jim?)<br />
* Run on some datasets<br />
* Write IJ paper<br />
* Submit<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h1>Progress</h1><br />
* the spherical param. filters are now more robust and way faster<br />
* the QE triangular mesh subdivision filter is complete and tested.<br />
* a bug has been found, corrected and commited to ITK<br />
<br />
</div><br />
<br />
<br style="clear: both;" /><br />
<br />
</div><br />
<br />
===References===<br />
#A. GELAS, A. GOUAILLARD, S. MEGASON, "Triangular Meshes Delaunay Conforming Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
#A. GELAS, A. GOUAILLARD, S. MEGASON, "Mutable Priority Queue Container", Insight Journal, Vol. 9, Jan.-Jun. '08.<br />
#A. GELAS, A. GOUAILLARD, "Parameterization of discrete surfaces", Insight Journal, Vol. 8, July - December '07.<br />
#A. GOUAILLARD, L. FLOREZ, E. BOIX, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, Insight Journal, Vol. 5, July - Dec. '06.</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=2009_Winter_Project_Week_Surface_Processing&diff=344122009 Winter Project Week Surface Processing2009-01-07T15:35:54Z<p>Agouaillard: /* Key Investigators */</p>
<hr />
<div>{|<br />
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]<br />
|[[]]<br />
|[[]]<br />
|}<br />
<br />
<br />
__NOTOC__<br />
<br />
<br />
===Key Investigators===<br />
* Arnaud Gelas, Harvard Medical School<br />
* Alexandre Gouaillard, Harvard Medical School<br />
* Luis Ibanez<br />
<br />
<div style="margin: 20px;"><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Objective</h1><br />
<br />
* Implement<br />
* Test<br />
* run on examples<br />
* Write corresponding IJ paper<br />
* submit to IJ<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Approach, Plan</h1><br />
* Filters are already implemented<br />
* Code Review with an ITK expert (luis/bill/jim?)<br />
* Run on some datasets<br />
* Write IJ paper<br />
* Submit<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h1>Progress</h1><br />
<br />
<br />
</div><br />
<br />
<br style="clear: both;" /><br />
<br />
</div><br />
<br />
===References===<br />
#A. GELAS, A. GOUAILLARD, S. MEGASON, "Triangular Meshes Delaunay Conforming Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
#A. GELAS, A. GOUAILLARD, S. MEGASON, "Mutable Priority Queue Container", Insight Journal, Vol. 9, Jan.-Jun. '08.<br />
#A. GELAS, A. GOUAILLARD, "Parameterization of discrete surfaces", Insight Journal, Vol. 8, July - December '07.<br />
#A. GOUAILLARD, L. FLOREZ, E. BOIX, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, Insight Journal, Vol. 5, July - Dec. '06.</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=AHM2009:Meshing_Breakout&diff=34315AHM2009:Meshing Breakout2009-01-06T14:59:10Z<p>Agouaillard: </p>
<hr />
<div> Back to [[AHM_2009]]<br />
<br />
Breakout session Moderator: Steve Pieper<br />
<br />
Topics:<br />
* Mesh Generation <br />
** Hexahedral<br />
** Tetrahedral<br />
** Open Source Tools<br />
* Applications<br />
** Cardiology<br />
** Orthopedics<br />
** Neurosurgery<br />
** Vascular disease and vascular surgery<br />
<br />
Attendees (anyone interested, please sign up):<br />
* Andriy Fedorov<br />
* Allen Tannenbaum<br />
* Curt Lisle<br />
* Vince Magnotta<br />
* Nicole Grosland<br />
* Steve Pieper<br />
* Ron Kikinis<br />
* Saikat Pal<br />
* Harish<br />
* Jeroen Stinstra<br />
* Luca Antiga<br />
* alex. gouaillard</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=AHM2009:Cell_Segmentation&diff=34312AHM2009:Cell Segmentation2009-01-06T14:57:42Z<p>Agouaillard: </p>
<hr />
<div>Back to [[AHM_2009]]<br />
<br />
Breakout session Moderator: Alexandre Gouaillard<br />
<br />
Agenda: ITK Extensions for cell segmentation:<br />
<br />
*specific "edge-free" level set implementation - Kishore<br />
*optimization of multi-target level set (application to cell tracking) - kishore<br />
*Manual segmentation Widgets for 3D cells - arnaud<br />
*FastICA unmixing filter - arnaud</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=33727MegasonLab2008-12-16T18:41:08Z<p>Agouaillard: /* The Megason Lab */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
*Gelas, Gouaillard, Megason, "Surface Mesh Discrete Curvature Estimators", [[http://hdl.handle.net/1926/1494 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Surface Mesh Normals Filter", [[http://hdl.handle.net/1926/1495 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Surface Meshes Incremental Decimation Framework", [[http://hdl.handle.net/1926/1488 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Triangular Meshes Delaunay Conforming Filter", [[http://hdl.handle.net/1926/1489 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Mutable Priority Queue Container", [[http://hdl.handle.net/1926/1395 Insight Journal]]<br />
*Gelas, Gouaillard, "Parameterization of discrete surfaces", [[http://hdl.handle.net/1926/1315 Insight Journal]]<br />
*Gouaillard , Brown, Bronner-Fraser, Fraser, Megason, "GoFigure and The Digital Fish Project: Open tools and open data for an imaging based approach to system biology", [[http://hdl.handle.net/1926/565 Insight Journal]]<br />
*Gouaillard, Florez, Boix, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, [[http://hdl.handle.net/1926/306 Insight Journal ]]<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2009_Winter_Project_Week|2009 January: Project Event 8]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti) <br><br />
[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard) <br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas) <br><br />
<br />
<br />
----<br />
[[AHM2009:Cell Segmentation|Cell Segmentation breakout session]] (Alex G, arnaud G, Kishore M)<br />
<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Summer_Project_Week|2008 June: Project Event 7]] ==<br />
This event is scheduled for <br />
<br />
----<br />
<br />
<br />
----<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
<br />
----<br />
<br />
We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
<br />
|-<br />
| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
| |<br />
<br />
== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
<br />
----<br />
<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=33726MegasonLab2008-12-16T18:39:29Z<p>Agouaillard: /* The Megason Lab */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
*A. Gelas, A. Gouaillard, S. Megason, "Surface Mesh Discrete Curvature Estimators", [[http://hdl.handle.net/1926/1494 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Normals Filter", [[http://hdl.handle.net/1926/1495 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Meshes Incremental Decimation Framework", [[http://hdl.handle.net/1926/1488 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Triangular Meshes Delaunay Conforming Filter", [[http://hdl.handle.net/1926/1489 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Mutable Priority Queue Container", [[http://hdl.handle.net/1926/1395 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, "Parameterization of discrete surfaces", [[http://hdl.handle.net/1926/1315 Insight Journal]]<br />
*Gouaillard A.; Brown T.; Bronner-Fraser M.; Fraser S.; Megason S "GoFigure and The Digital Fish Project: Open tools and open data for an imaging based approach to system biology", [[http://hdl.handle.net/1926/565 Insight Journal]]<br />
<br />
. <br />
*A. GOUAILLARD, L. FLOREZ, E. BOIX, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, [[http://hdl.handle.net/1926/306 Insight Journal ]]<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2009_Winter_Project_Week|2009 January: Project Event 8]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti) <br><br />
[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard) <br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas) <br><br />
<br />
<br />
----<br />
[[AHM2009:Cell Segmentation|Cell Segmentation breakout session]] (Alex G, arnaud G, Kishore M)<br />
<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Summer_Project_Week|2008 June: Project Event 7]] ==<br />
This event is scheduled for <br />
<br />
----<br />
<br />
<br />
----<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
<br />
----<br />
<br />
We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
<br />
|-<br />
| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
| |<br />
<br />
== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
<br />
----<br />
<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=33725MegasonLab2008-12-16T18:36:52Z<p>Agouaillard: /* The Megason Lab */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Discrete Curvature Estimators", [[http://hdl.handle.net/1926/1494 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Normals Filter", [[http://hdl.handle.net/1926/1495 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Meshes Incremental Decimation Framework", [[http://hdl.handle.net/1926/1488 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Triangular Meshes Delaunay Conforming Filter", [[http://hdl.handle.net/1926/1489 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Mutable Priority Queue Container", [[http://hdl.handle.net/1926/1395 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, "Parameterization of discrete surfaces", [[http://hdl.handle.net/1926/1315 Insight Journal]]<br />
*A. GOUAILLARD, L. FLOREZ, E. BOIX, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, [[http://hdl.handle.net/1926/306 Insight Journal ]]<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2009_Winter_Project_Week|2009 January: Project Event 8]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti) <br><br />
[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard) <br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas) <br><br />
<br />
<br />
----<br />
[[AHM2009:Cell Segmentation|Cell Segmentation breakout session]] (Alex G, arnaud G, Kishore M)<br />
<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Summer_Project_Week|2008 June: Project Event 7]] ==<br />
This event is scheduled for <br />
<br />
----<br />
<br />
<br />
----<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
<br />
----<br />
<br />
We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
<br />
|-<br />
| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
| |<br />
<br />
== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
<br />
----<br />
<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=33724MegasonLab2008-12-16T18:36:34Z<p>Agouaillard: /* The Megason Lab */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Discrete Curvature Estimators", [[http://hdl.handle.net/1926/1494 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Normals Filter", [[http://hdl.handle.net/1926/1495 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Meshes Incremental Decimation Framework", [[http://hdl.handle.net/1926/1488 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Triangular Meshes Delaunay Conforming Filter", [[http://hdl.handle.net/1926/1489 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Mutable Priority Queue Container", [[http://hdl.handle.net/1926/1395 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, "Parameterization of discrete surfaces", [[http://hdl.handle.net/1926/1315 Insight Journal<br />
*A. GOUAILLARD, L. FLOREZ, E. BOIX, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, [[http://hdl.handle.net/1926/306 Insight Journal ]]<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2009_Winter_Project_Week|2009 January: Project Event 8]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti) <br><br />
[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard) <br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas) <br><br />
<br />
<br />
----<br />
[[AHM2009:Cell Segmentation|Cell Segmentation breakout session]] (Alex G, arnaud G, Kishore M)<br />
<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Summer_Project_Week|2008 June: Project Event 7]] ==<br />
This event is scheduled for <br />
<br />
----<br />
<br />
<br />
----<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
<br />
----<br />
<br />
We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
<br />
|-<br />
| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
| |<br />
<br />
== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
<br />
----<br />
<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=33723MegasonLab2008-12-16T18:33:58Z<p>Agouaillard: /* The Megason Lab */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Discrete Curvature Estimators", [[http://hdl.handle.net/1926/306 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Normals Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Meshes Incremental Decimation Framework", [[http://hdl.handle.net/1926/1488 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Triangular Meshes Delaunay Conforming Filter", [[http://hdl.handle.net/1926/1489 Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Mutable Priority Queue Container", Insight Journal, Vol. 9, Jan.-Jun. '08.<br />
*A. GELAS, A. GOUAILLARD, "Parameterization of discrete surfaces", Insight Journal, Vol. 8, July - December '07.<br />
*A. GOUAILLARD, L. FLOREZ, E. BOIX, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, [[http://hdl.handle.net/1926/306 Insight Journal ]]<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2009_Winter_Project_Week|2009 January: Project Event 8]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti) <br><br />
[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard) <br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas) <br><br />
<br />
<br />
----<br />
[[AHM2009:Cell Segmentation|Cell Segmentation breakout session]] (Alex G, arnaud G, Kishore M)<br />
<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Summer_Project_Week|2008 June: Project Event 7]] ==<br />
This event is scheduled for <br />
<br />
----<br />
<br />
<br />
----<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
<br />
----<br />
<br />
We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
<br />
|-<br />
| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
| |<br />
<br />
== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
<br />
----<br />
<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=33722MegasonLab2008-12-16T18:29:31Z<p>Agouaillard: /* The Megason Lab */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Discrete Curvature Estimators", [[http://hdl.handle.net/1926/306 |Insight Journal]]<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Normals Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Meshes Incremental Decimation Framework", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Triangular Meshes Delaunay Conforming Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Mutable Priority Queue Container", Insight Journal, Vol. 9, Jan.-Jun. '08.<br />
*A. GELAS, A. GOUAILLARD, "Parameterization of discrete surfaces", Insight Journal, Vol. 8, July - December '07.<br />
*A. GOUAILLARD, L. FLOREZ, E. BOIX, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, Insight Journal, Vol. 5, July - Dec. '06.<br />
<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2009_Winter_Project_Week|2009 January: Project Event 8]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti) <br><br />
[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard) <br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas) <br><br />
<br />
<br />
----<br />
[[AHM2009:Cell Segmentation|Cell Segmentation breakout session]] (Alex G, arnaud G, Kishore M)<br />
<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Summer_Project_Week|2008 June: Project Event 7]] ==<br />
This event is scheduled for <br />
<br />
----<br />
<br />
<br />
----<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
<br />
----<br />
<br />
We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
<br />
|-<br />
| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
| |<br />
<br />
== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
<br />
----<br />
<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=33721MegasonLab2008-12-16T18:07:40Z<p>Agouaillard: /* 2008 June: Project Event 7 */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Discrete Curvature Estimators", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Normals Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Meshes Incremental Decimation Framework", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Triangular Meshes Delaunay Conforming Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Mutable Priority Queue Container", Insight Journal, Vol. 9, Jan.-Jun. '08.<br />
*A. GELAS, A. GOUAILLARD, "Parameterization of discrete surfaces", Insight Journal, Vol. 8, July - December '07.<br />
*A. GOUAILLARD, L. FLOREZ, E. BOIX, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, Insight Journal, Vol. 5, July - Dec. '06.<br />
<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2009_Winter_Project_Week|2009 January: Project Event 8]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti) <br><br />
[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard) <br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas) <br><br />
<br />
<br />
----<br />
[[AHM2009:Cell Segmentation|Cell Segmentation breakout session]] (Alex G, arnaud G, Kishore M)<br />
<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Summer_Project_Week|2008 June: Project Event 7]] ==<br />
This event is scheduled for <br />
<br />
----<br />
<br />
<br />
----<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
<br />
----<br />
<br />
We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
<br />
|-<br />
| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
| |<br />
<br />
== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
<br />
----<br />
<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=33718MegasonLab2008-12-16T18:02:31Z<p>Agouaillard: </p>
<hr />
<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Discrete Curvature Estimators", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Normals Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Meshes Incremental Decimation Framework", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Triangular Meshes Delaunay Conforming Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Mutable Priority Queue Container", Insight Journal, Vol. 9, Jan.-Jun. '08.<br />
*A. GELAS, A. GOUAILLARD, "Parameterization of discrete surfaces", Insight Journal, Vol. 8, July - December '07.<br />
*A. GOUAILLARD, L. FLOREZ, E. BOIX, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, Insight Journal, Vol. 5, July - Dec. '06.<br />
<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2009_Winter_Project_Week|2009 January: Project Event 8]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti) <br><br />
[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard) <br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas) <br><br />
<br />
<br />
----<br />
[[AHM2009:Cell Segmentation|Cell Segmentation breakout session]] (Alex G, arnaud G, Kishore M)<br />
<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Summer_Project_Week|2008 June: Project Event 7]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
<br />
----<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
<br />
----<br />
<br />
We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
<br />
|-<br />
| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
| |<br />
<br />
== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
<br />
----<br />
<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=33717MegasonLab2008-12-16T18:01:54Z<p>Agouaillard: /* 2009 January: Project Event 7 */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Discrete Curvature Estimators", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Normals Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Meshes Incremental Decimation Framework", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Triangular Meshes Delaunay Conforming Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Mutable Priority Queue Container", Insight Journal, Vol. 9, Jan.-Jun. '08.<br />
*A. GELAS, A. GOUAILLARD, "Parameterization of discrete surfaces", Insight Journal, Vol. 8, July - December '07.<br />
*A. GOUAILLARD, L. FLOREZ, E. BOIX, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, Insight Journal, Vol. 5, July - Dec. '06.<br />
<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2009_Winter_Project_Week|2009 January: Project Event 8]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti) <br><br />
[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard) <br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas) <br><br />
<br />
<br />
----<br />
[[AHM2009:Cell Segmentation|Cell Segmentation breakout session]] (Alex G, arnaud G, Kishore M)<br />
<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Summer_Project_Week|2008 June: Project Event 7]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
<br />
----<br />
<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
<br />
----<br />
<br />
We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
<br />
|-<br />
| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
| |<br />
<br />
== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
<br />
----<br />
<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=33716MegasonLab2008-12-16T17:59:56Z<p>Agouaillard: </p>
<hr />
<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Discrete Curvature Estimators", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Normals Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Meshes Incremental Decimation Framework", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Triangular Meshes Delaunay Conforming Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Mutable Priority Queue Container", Insight Journal, Vol. 9, Jan.-Jun. '08.<br />
*A. GELAS, A. GOUAILLARD, "Parameterization of discrete surfaces", Insight Journal, Vol. 8, July - December '07.<br />
*A. GOUAILLARD, L. FLOREZ, E. BOIX, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, Insight Journal, Vol. 5, July - Dec. '06.<br />
<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2009_Winter_Project_Week|2009 January: Project Event 8]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti) <br><br />
[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard) <br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas) <br><br />
<br />
<br />
----<br />
[[AHM2009:Cell Segmentation|Cell Segmentation breakout session]] (Alex G, arnaud G, Kishore M)<br />
<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Winter_Project_Week|2009 January: Project Event 7]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
<br />
----<br />
<br />
<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
<br />
----<br />
<br />
We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
<br />
|-<br />
| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
| |<br />
<br />
== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
<br />
----<br />
<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=33715MegasonLab2008-12-16T17:54:52Z<p>Agouaillard: </p>
<hr />
<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Discrete Curvature Estimators", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Normals Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Meshes Incremental Decimation Framework", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Triangular Meshes Delaunay Conforming Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Mutable Priority Queue Container", Insight Journal, Vol. 9, Jan.-Jun. '08.<br />
*A. GELAS, A. GOUAILLARD, "Parameterization of discrete surfaces", Insight Journal, Vol. 8, July - December '07.<br />
*A. GOUAILLARD, L. FLOREZ, E. BOIX, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, Insight Journal, Vol. 5, July - Dec. '06.<br />
<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2009_Winter_Project_Week|2009 January: Project Event 8]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti) <br><br />
[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard) <br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas) <br><br />
<br />
<br />
----<br />
[[AHM2009:Cell Segmentation|Cell Segmentation breakout session]] (Alex G, arnaud G, Kishore M)<br />
<br />
<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
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<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
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We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
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| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
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== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
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<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]</div>Agouaillardhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=33714MegasonLab2008-12-16T17:43:13Z<p>Agouaillard: </p>
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<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Discrete Curvature Estimators", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Mesh Normals Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Surface Meshes Incremental Decimation Framework", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Triangular Meshes Delaunay Conforming Filter", Insight Journal, Vol. 10, July - Dec. '08.<br />
*A. GELAS, A. GOUAILLARD, S. MEGASON, "Mutable Priority Queue Container", Insight Journal, Vol. 9, Jan.-Jun. '08.<br />
*A. GELAS, A. GOUAILLARD, "Parameterization of discrete surfaces", Insight Journal, Vol. 8, July - December '07.<br />
*A. GOUAILLARD, L. FLOREZ, E. BOIX, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, Insight Journal, Vol. 5, July - Dec. '06.<br />
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|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
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<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
<br />
----<br />
<br />
We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
<br />
|-<br />
| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
| |<br />
<br />
== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
<br />
----<br />
<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]</div>Agouaillard