https://www.na-mic.org/w/api.php?action=feedcontributions&user=Arnaudgelas&feedformat=atomNAMIC Wiki - User contributions [en]2024-03-29T10:43:00ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week&diff=554262010 Summer Project Week2010-06-25T14:44:54Z<p>Arnaudgelas: /* Microscopy Image Analysis */</p>
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<div>Back to [[Project Events]], [[Events]]<br />
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[[Image:PW-MIT2010.png|500px|right]]<br />
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__TOC__<br />
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[http://www.smugmug.com/gallery/12687574_DsJjF '''Photos ''']<br />
<br><br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background: #b0d5e6; color: #02186f; font-size: 130%" <br />
!Time<br />
!width="250px"|Monday, June 21<br />
!width="250px"|Tuesday, June 22<br />
!width="250px"|Wednesday, June 23<br />
!width="250px"|Thursday, June 24<br />
!width="250px"|Friday, June 25<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''9am:''' [[Media:NAMIC Kit-2010-6-22.ppt|NA-MIC Kit Update]] (Jim Miller)<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''9:20am:''' [[Media:2010_Project_Week_Slicer.ppt|3D Slicer Update]] (Steve Pieper)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''10am:''' Superbuild Demo (Dave Partyka)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''10:15am:''' Break<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''10:30-11am:''' [[Media:2010_Project_Week_OpenIGTLink.ppt|OpenIGTLink Update]] (Junichi Tokuda)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''11am-12pm:''' [[2010_Summer_Project_Week_Slicer_Hands-on_Workshop|Slicer Hands-on Workshop]] (Randy Gollub, Sonia Pujol)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
|'''9am-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-5:30pm: Tutorial:''' [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)<br />
<br>[[MIT_Project_Week_Rooms#32-155|32-155 (Stata Lecture Hall)]]<br />
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> QT/Slicer (Steve, JC, J2)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
<br>----------------------------------------<br><br />
'''3-4pm:''' [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''4-5pm: <font color="#4020ff">Breakout Session:'''</font><br />
<br> [[2010 Summer Project Week Breakout Session: Data Management |Data Management]] (Stephen Aylward)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
|'''12:45-1pm:''' [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)<br />
<br>[[MIT_Project_Week_Rooms#Kiva|Kiva Room]]<br />
<br>----------------------------------------<br><br />
'''3-5pm: <font color="#4020ff">Breakout Session:'''</font><br><br />
[[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
<br>----------------------------------------<br><br />
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widgets]] (Nicole, Kilian, JC)<br />
<br>[[MIT_Project_Week_Rooms#32-261|32-261 Room]]<br />
<br>----------------------------------------<br><br />
<br>'''5pm: <font color="#4020ff">Reception'''</font><br> <br />
<br>[[MIT_Project_Week_Rooms#R&D Pub|R&D Pub]]<br />
|'''1-2pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)<br />
<br>----------------------------------------<br><br />
'''2-3pm:''' Simple Git (Steve Pieper) [[media:Simple Git-pieper-2010-06-24.ppt|(Slides)]] <br />
<br>----------------------------------------<br><br />
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> <br />
[[2010 Summer Project Week Breakout Session: Volume Rendering|Volume Rendering Demos and Discussion]] (Yin Wu, Steve Pieper)<br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
Please note:<br />
*We need to empty room by 1:30pm on Friday. 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| January 3-7, 2011, Salt Lake City, 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_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)<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_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_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)<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/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Johannes Schick, Steve Pieper, Ron Kikinis)<br />
<br />
=== Registration ===<br />
#[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)<br />
#[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)<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_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)<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, Andriy Fedorov)<br />
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)<br />
<br />
=== Shape Analysis ===<br />
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)<br />
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)<br />
# [[2010_Summer_Project_Week_Shape_Analysis_UNC|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 />
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)<br />
<br />
=== Diffusion ===<br />
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)<br />
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)<br />
#[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)<br />
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)<br />
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)<br />
<br />
=== IGT ===<br />
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)<br />
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)<br />
#[[2010_Summer_Project_Week_Prostate_Intervention|Prostate Intervention(Junichi Tokuda, Tamas Ungi, Haiying Liu, Sam Song)]]<br />
#[[2010_Summer_Project_Week_Liver_Ablation|Liver Ablation (Haiying Liu, Noby Hata)]]<br />
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)<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, Masakatsu Hoashi, Junichi Tokuda, Noby Hata)<br />
#[[2010_Summer_Project_Week_Tracking_Neuroendoscope_Using_EM_Tracker_and_OpenIGTLink|Tracking Neuroendoscope Using EM Tracker and OpenIGTLink]] (Laurent Chauvin, Junichi Tokuda, Noby Hata)<br />
#[[2010_Summer_Project_Week_Implementing_OpenCV_to_Slicer3_for_Neuroendoscopic_Surgery|Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery]] (Atsushi Yamada, Junichi Tokuda, 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 />
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)<br />
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)<br />
#[[2010_Summer_Project_Week_Mouse_Brain_Cortical_Thickness_Analysis|Mouse brain cortical thickness analysis]] (Joohwi Lee, Ipek Oguz, Martin Styner)<br />
#[[2010_Summer_Project_Week_Primate image analysis using the standard Slicer pipeline|Primate image analysis using the standard Slicer pipeline]] (Yundi Shi, Martin Styner, Andriy Fedorov)<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 />
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnotta, Peter Karasev, Curt Lisle, Ron Kikinis) <br />
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)<br />
#[[2010_Summer_Project_Week_Quantification_Of_Lesion_Diffusion_Disruption| Quantification of Lesion Diffusion Disruption]](M Scully, H J Bockholt)<br />
#[[2010_Summer_Project_Week_Lupus_Lesion_Segmentation_and_Review_Statistics|Lupus Lesion Segmentation and Review Statistics]](M Scully, H J Bockholt)<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 />
# [[Import/Export Farsight-GoFigure results]] (Arnaud Gelas, Lydie Souhait, Kedar Grama, Raghav Padmanabhan, Sean Megason, Badri Roysam)<br />
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)<br />
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Kishore Mosaliganti, Arnaud Gelas, Sean Megason, Raghu Machiraju)<br />
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)<br />
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Arnaud Gelas, Stever Pieper)<br />
# [[Seedings results comparison]] (Antonin Perrot-Audet, Raghav Padmanabhan, 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 />
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)<br />
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)<br />
<br />
=== NA-MIC Kit Internals ===<br />
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)<br />
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)<br />
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andriy Fedorov, Yanling Liu, Alex Yarmarkovich, Jim Barabas)<br />
#[[2010 NAMIC Project week:Inventory of Volume Rendering Functionality|Inventory of Volume Rendering Functionality]] (Jim Barabas, Noby Hata)<br />
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)<br />
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)<br />
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)<br />
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)<br />
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]](David Partyka, Steve Pieper, Katie Hayes)<br />
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)<br />
#[[2010 NAMIC Project week: Real-Time Volume Rendering for Virtual Colonoscopy|Real-Time Volume Rendering for Virtual Colonoscopy]] (Hiro Yoshida, Yin Wu, Steve Pieper, Ron Kikinis)<br />
<br />
=== Workflows and Integration ===<br />
# [[Summer_project_week_2010_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)<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 />
<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 />
# Yousef Al-Kofahi , CompuCyte Corporation<br />
# Peter Anderson , retired<br />
# Nicole Aucoin , BWH<br />
# Michel Audette , Kitware<br />
# Stephen Aylward , Kitware, Inc<br />
# Jim Barabas, MIT<br />
#Barrett, Ryan, BWH<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 />
#Nikos Chrisochoides, College of William and Mary<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 />
# Randy Gollub , MGH<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 />
#Masakatsu Hoashi, 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 />
#Peter Karasev, Georgia Tech<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 />
# Joohwi Lee , UNC Chapel Hill<br />
# Rui Li , MGH<br />
# Stefan Lienhard , LMI<br />
# Curtis Lisle , KnowledgeVis, LLC<br />
# Haiying Liu , Brigham and Women's Hospital<br />
# Felix Liu , Beth Israel Deaconess Medical Center<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 />
#Charles Maneval, BWH<br />
# Daniel Marcus , Washington University<br />
# William Marks , Focused Ultrasound Lab, BWH, HMS<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 />
# Beck Olson , UCSF<br />
# John Onofrey , Yale University<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 />
# Eun-Joo Park , Brigham & Women's Hospital<br />
# David Partyka , Kitware Inc<br />
# Pratik Patel , <br />
# Sudhir Pathak , Univeristy Of Pittsburgh<br />
# Thierry PECOT , Ohio State University<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 />
# Johannes Schick , SPL<br />
# William Schroeder , Kitware<br />
# Mark Scully , The Mind Research Network<br />
#Gunasekaran Seetharaman, US Air Force Research Lab<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 />
# Matthew Toews , Brigham and Women's Hospital, Harvard Medical School<br />
# Junichi Tokuda , Brigham and Women's Hospital<br />
# Tamas Ungi , Queen's University<br />
# Clement Vachet , UNC Chapel Hill<br />
# Veda Vadyar , Brigham and Women's Hospital<br />
# Gopalkrishna Veni , SCI Institute<br />
# Stuart Wallace , Massachusetts General Hospital<br />
# Demian Wassermann , SPL/LMI/PNL<br />
#Yihan Wei, BWH<br />
# Adam Weinrich , Nokia<br />
# Sandy Wells , BWH<br />
# Phillip White , BWH/HMS<br />
# Guorong Wu , University of North Carolina at Chapel Hill<br />
# Yin Wu , Mass General Hospital<br />
# Atsushi Yamada , Nagoya Institute of Technology<br />
# Alexander Yarmarkovich , ISOMICS<br />
# Alexander Zaitsev , Brigham and Womens Hospital</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Import/Export_Farsight-GoFigure_results&diff=55382Import/Export Farsight-GoFigure results2010-06-25T14:12:35Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Lydie Souhait, Arnaud Gelas, Sean Megason<br />
* RPI: Kedar Grama, Raghav Padmanabhan, Badri Roysam<br />
<br />
==Project==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Exchange data (cell segmentation results) between Farsight and Gofigure2<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Discuss current status of both projects<br />
* Define common objects/traces used by both projects<br />
* Install both projects<br />
* Export the data from both projects into textfiles<br />
* Import the data from Farsight into Gofigure Database<br />
* Import the data from Gofigure Database into Farsight<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Export Contours/Meshes from Gofigure2 into textfile done<br />
* Import Contours/Meshes from textfile into Gofigure2 database done<br />
* Import segmentation results from Farsight into Gofigurew done<br />
* Import results from Gofigure2 into Farsight ~75% done <br />
</div><br />
</div><br />
<br />
http://github.com/arnaudgelas/SegmentationToGoFigure2<br />
<br />
<br />
<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Import/Export_Farsight-GoFigure_results&diff=55380Import/Export Farsight-GoFigure results2010-06-25T14:11:55Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Lydie Souhait, Arnaud Gelas, Sean Megason<br />
* RPI: Raghav Padmanabhan, Badri Roysam<br />
<br />
==Project==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Exchange data (cell segmentation results) between Farsight and Gofigure2<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Discuss current status of both projects<br />
* Define common objects/traces used by both projects<br />
* Install both projects<br />
* Export the data from both projects into textfiles<br />
* Import the data from Farsight into Gofigure Database<br />
* Import the data from Gofigure Database into Farsight<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Export Contours/Meshes from Gofigure2 into textfile done<br />
* Import Contours/Meshes from textfile into Gofigure2 database done<br />
* Import segmentation results from Farsight into Gofigurew done<br />
* Import results from Gofigure2 into Farsight ~75% done <br />
</div><br />
</div><br />
<br />
http://github.com/arnaudgelas/SegmentationToGoFigure2<br />
<br />
<br />
<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week&diff=547232010 Summer Project Week2010-06-21T01:46:03Z<p>Arnaudgelas: /* Microscopy Image Analysis */</p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
<br />
[[Image:PW-MIT2010.png|500px|right]]<br />
<br />
__TOC__<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background: #b0d5e6; color: #02186f; font-size: 130%" <br />
!Time<br />
!width="250px"|Monday, June 21<br />
!width="250px"|Tuesday, June 22<br />
!width="250px"|Wednesday, June 23<br />
!width="250px"|Thursday, June 24<br />
!width="250px"|Friday, June 25<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''9am:''' NA-MIC Kit Update (Jim Miller) <br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''9:45am:''' [[Media:2010_Project_Week_Slicer.ppt|3D Slicer Update]] (Steve Pieper)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''10:30-11am:''' OpenIGTLink Update (Junichi Tokuda)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''11am-12pm:''' Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room A]]<br />
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)<br />
|'''9am-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-5:30pm: Tutorial:''' [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)<br />
<br>[[MIT_Project_Week_Rooms#32-155|32-155 (Stata Lecture Hall)]]<br />
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> QT/Slicer (Steve, JC, J2)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
<br>----------------------------------------<br><br />
'''3-4pm:''' [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''4-5pm: <font color="#4020ff">Breakout Session:'''</font><br />
<br> [[2010 Summer Project Week Breakout Session: Data Management |Data Management]] (Dan Marcus, Stephen Aylward)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
|'''12:45-1pm:''' [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]<br />
<br>----------------------------------------<br><br />
'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)<br />
<br>----------------------------------------<br><br />
'''3-5pm: <font color="#4020ff">Breakout Session:'''</font><br><br />
[[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)<br />
<br>----------------------------------------<br><br />
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widgets]] (Nicole, Kilian, JC)<br />
|'''1-2pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)<br />
<br>----------------------------------------<br><br />
'''2-3pm:''' Build Instructions: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)<br />
<br>----------------------------------------<br><br />
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> <br />
[[2010 Summer Project Week Breakout Session: Volume Rendering|Volume Rendering Demos and Discussion]] (Yin Wu, Steve Pieper)<br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
<br />
Please note:<br />
*We need to empty room by 1:30pm on Friday. 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| January 3-7, 2011, Salt Lake City, 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_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)<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_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_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)<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/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 />
<br />
<br />
=== Registration ===<br />
#[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)<br />
#[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)<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_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)<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, Andriy Fedorov)<br />
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)<br />
<br />
=== Shape Analysis ===<br />
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)<br />
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)<br />
# [[2010_Summer_Project_Week_Shape_Analysis_UNC|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 />
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)<br />
<br />
=== Diffusion ===<br />
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)<br />
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)<br />
#[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)<br />
#[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)<br />
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)<br />
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)<br />
<br />
=== IGT ===<br />
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)<br />
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)<br />
#[[2010_Summer_Project_Week_Prostate_Intervention|Prostate Intervention(Junichi, Sam Song, Tamas Ungi)]]<br />
#[[2010_Summer_Project_Week_Liver_Ablation|Liver Ablation (Haiying Liu, Noby Hata)]]<br />
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)<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 />
#[[2010_Summer_Project_Week_Tracking_Neuroendoscope_Using_EM_Tracker_and_OpenIGTLink|Tracking Neuroendoscope Using EM Tracker and OpenIGTLink]] (Laurent Chauvin, Junichi Tokuda, Noby Hata)<br />
#[[2010_Summer_Project_Week_Implementing_OpenCV_to_Slicer3_for_Neuroendoscopic_Surgery|Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery]] (Atsushi Yamada, Junichi Tokuda, 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 />
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)<br />
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)<br />
#[[2010_Summer_Project_Week_Mouse_Brain_Cortical_Thickness_Analysis|Mouse brain cortical thickness analysis]] (Joohwi Lee, Ipek Oguz, Martin Styner)<br />
#[[2010_Summer_Project_Week_Primate image analysis using the standard Slicer pipeline|Primate image analysis using the standard Slicer pipeline]] (Yundi Shi, Martin Styner, Andriy Fedorov)<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 />
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnotta, Peter Karasev, Curt Lisle, Ron Kikinis) <br />
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)<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 />
# [[Import/Export Farsight-GoFigure results]] ( Arnaud Gelas, Lydie Souhait, Raghav Padmanabhan, Sean Megason, Badri Roysam)<br />
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)<br />
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Kishore Mosaliganti, Arnaud Gelas, Sean Megason, Raghu Machiraju)<br />
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)<br />
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Arnaud Gelas, Stever Pieper)<br />
# [[Seedings results comparison]] (Antonin Perrot-Audet, Raghav Padmanabhan, 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 />
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)<br />
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)<br />
<br />
=== NA-MIC Kit Internals ===<br />
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)<br />
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)<br />
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andriy Fedorov, Yanling Liu, Alex Yarmarkovich, Jim Barabas)<br />
#[[2010 NAMIC Project week:Inventory of Volume Rendering Functionality|Inventory of Volume Rendering Functionality]] (Jim Barabas)<br />
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)<br />
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)<br />
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)<br />
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)<br />
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]](David Partyka, Steve Pieper, Katie Hayes)<br />
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)<br />
#[[2010 NAMIC Project week: Volume Rendering for Virtual Colonoscopy|Volume Rendering for Virtual Colonoscopy]] (Hiro Yoshida, Yin Wu, Steve Piper, Ron Kikinis)<br />
<br />
=== Workflows and Integration ===<br />
# [[Summer_project_week_2010_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)<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 />
<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 />
# Yousef Al-Kofahi , CompuCyte Corporation<br />
# Peter Anderson , retired<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 />
# Randy Gollub , MGH<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 />
# Joohwi Lee , UNC Chapel Hill<br />
# Rui Li , MGH<br />
# Stefan Lienhard , LMI<br />
# Curtis Lisle , KnowledgeVis, LLC<br />
# Haiying Liu , Brigham and Women's Hospital<br />
# Felix Liu , Beth Israel Deaconess Medical Center<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 />
# William Marks , Focused Ultrasound Lab, BWH, HMS<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 />
# Beck Olson , UCSF<br />
# John Onofrey , Yale University<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 />
# Eun-Joo Park , Brigham & Women's Hospital<br />
# David Partyka , Kitware Inc<br />
# Pratik Patel , <br />
# Sudhir Pathak , Univeristy Of Pittsburgh<br />
# Thierry PECOT , Ohio State University<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 />
# Johannes Schick , SPL<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 />
# Matthew Toews , Brigham and Women's Hospital, Harvard Medical School<br />
# Junichi Tokuda , Brigham and Women's Hospital<br />
# Tamas Ungi , Queen's University<br />
# Clement Vachet , UNC Chapel Hill<br />
# Veda Vadyar , Brigham and Women's Hospital<br />
# Gopalkrishna Veni , SCI Institute<br />
# Stuart Wallace , Massachusetts General Hospital<br />
# Demian Wassermann , SPL/LMI/PNL<br />
# Adam Weinrich , Nokia<br />
# Sandy Wells , BWH<br />
# Phillip White , BWH/HMS<br />
# Guorong Wu , University of North Carolina at Chapel Hill<br />
# Yin Wu , Mass General Hospital<br />
# Atsushi Yamada , Nagoya Institute of Technology<br />
# Alexander Yarmarkovich , ISOMICS<br />
# Alexander Zaitsev , Brigham and Womens Hospital</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=MedianTexture&diff=54689MedianTexture2010-06-20T22:38:09Z<p>Arnaudgelas: </p>
<hr />
<div>__NOTOC__<br />
[[File:MBP-definition.jpg|400px|thumb|left|Definition of MBP]]<br />
<gallery><br />
Image:2TS0005_stack0001frame0005.png|Original PCNA-GFP fluorescence confocal microscope image for cell cycle marker studies.<br />
Image:FGPAC_mask_101iter_stack0001frame0005.png|Multiphase GPAC segmentation mask.<br />
Image:Masked-bkg mbp+2.png|Distribution of MBPs shown with each pattern mapped to a unique color.<br />
</gallery><br />
<gallery><br />
Image:MBP_2TS0005_5U.png|MBP Uniform pattern 5.<br />
Image:MBP_2TS0005_6U.png|MBP Uniform pattern 6.<br />
Image:MBP_2TS0005_7U.png|MBP Uniform pattern 7.<br />
</gallery><br />
<gallery><br />
Image:MBP_2TS0005_8U.png|MBP Uniform pattern 8.<br />
Image:MBP_2TS0005_13U.png|MBP Uniform pattern 13.<br />
Image:MBP_2TS0005_14U.png|MBP Uniform pattern 14.<br />
</gallery><br />
<gallery><br />
Image:MBP_2TS0005_15U.png|MBP Uniform pattern 15.<br />
Image:MBP_2TS0005_16U.png|MBP Uniform pattern 16.<br />
Image:MBP_2TS0005_17U.png|MBP Uniform pattern 17.<br />
</gallery><br />
<gallery><br />
Image:Mask_2TS0005_-1NU.png|MBP Non-Uniform pattern class.<br />
</gallery><br />
<br />
==Key Investigators==<br />
* ENSI-Bourges, France: Lucas Menand, Sarah Portugais, Adel Hafiane<br />
* Air Force Research Lab: Guna Seetharaman<br />
* University of Missouri: Filiz Bunyak, K. Palaniappan<br />
* Harvard: Sean Megason<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 40%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
Median binary patterns (MBP) are robust feature descriptors for characterizing natural and biological textures. MBPs can be used for cell segmentation, characterizing nuclei and membrane textures and for cell classification.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
MBPs is a robust alternative to the local binary pattern (LBP) texture descriptors that uses the local median instead of the central pixel intensity as the reference value to create a binary pattern. MBPs (and LBPs) have the attractive properties of noise-resistance, rotation invariance and shift-invariance and provide a powerful feature set for cell segmentation and classification. Using a 3x3 median window there are nine special median uniform patterns and a set of non-uniform patterns that we assign to a separate category.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
We have completed C++ and Matlab implementation of 2D median binary patterns and have a preliminary ITK version that needs to be tested and evaluated for correctness. Histograms of MBPs can be plotted using VTK widgets.<br />
<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 an:<br />
#ITK Module<br />
<br />
==References==<br />
*A. Hafiane, G. Seetharaman, K. Palaniappan, B. Zavidovique, “Rotationally invariant hashing of median patterns for texture classification”, Lecture Notes in Computer Science (ICIAR), Vol. 5112, 2008, pp. 619-629. <http://www.ncbi.nlm.nih.gov/pubmed/19116672><br />
<br />
*A. Hafiane, Seetharaman, G., Zavidovique, B.: Median binary pattern for textures classification. Lecture Notes in Computer Science CIAR, 2007, pp. 387–398.<br />
<br />
*T. Ojala, Pietikainen, M., Maenpaa, T.: Multiresolution gray-scale and rotation invariant texture classification with local binary patterns. IEEE Transactions on Pattern Analysis and Machine Intelligence 24(7), 2002, pp. 971–987.<br />
<br />
</div></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week&diff=546542010 Summer Project Week2010-06-20T14:18:07Z<p>Arnaudgelas: /* Microscopy Image Analysis */</p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
<br />
[[Image:PW-MIT2010.png|500px|right]]<br />
<br />
__TOC__<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background: #b0d5e6; color: #02186f; font-size: 130%" <br />
!Time<br />
!width="250px"|Monday, June 21<br />
!width="250px"|Tuesday, June 22<br />
!width="250px"|Wednesday, June 23<br />
!width="250px"|Thursday, June 24<br />
!width="250px"|Friday, June 25<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''9am:''' NA-MIC Kit Update (Jim Miller) <br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''9:45am:''' [[Media:2010_Project_Week_Slicer.ppt|3D Slicer Update]] (Steve Pieper)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''10:30-11am:''' OpenIGTLink Update (Junichi Tokuda)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''11am-12pm:''' Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room A]]<br />
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)<br />
|'''9am-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-5:30pm: Tutorial:''' [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)<br />
<br>[[MIT_Project_Week_Rooms#32-155|32-155 (Stata Lecture Hall)]]<br />
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> QT/Slicer (Steve, JC, J2)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
<br>----------------------------------------<br><br />
'''3-4pm:''' [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''4-5pm: <font color="#4020ff">Breakout Session:'''</font><br />
<br> [[2010 Summer Project Week Breakout Session: Data Management |Data Management]] (Dan Marcus, Stephen Aylward)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
|'''12:45-1pm:''' [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]<br />
<br>----------------------------------------<br><br />
'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)<br />
<br>----------------------------------------<br><br />
'''3-5pm: <font color="#4020ff">Breakout Session:'''</font><br><br />
[[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)<br />
<br>----------------------------------------<br><br />
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widgets]] (Nicole, Kilian, JC)<br />
|'''1-2pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)<br />
<br>----------------------------------------<br><br />
'''2-3pm:''' Build Instructions: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)<br />
<br>----------------------------------------<br><br />
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> <br />
[[2010 Summer Project Week Breakout Session: Volume Rendering|Volume Rendering Demos and Discussion]] (Yin Wu, Steve Pieper)<br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
<br />
Please note:<br />
*We need to empty room by 1:30pm on Friday. 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| January 3-7, 2011, Salt Lake City, 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, Andriy Fedorov)<br />
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)<br />
<br />
=== IGT ===<br />
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)<br />
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)<br />
#[[2010_Summer_Project_Week_Prostate_Intervention|Prostate Intervention(Junichi, Sam Song, Tamas Ungi)]]<br />
#[[2010_Summer_Project_Week_Liver_Ablation|Liver Ablation (Haiying Liu, Noby Hata)]]<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 />
#[[2010_Summer_Project_Week_Tracking_Neuroendoscope_Using_EM_Tracker_and_OpenIGTLink|Tracking Neuroendoscope Using EM Tracker and OpenIGTLink]] (Laurent Chauvin, Junichi Tokuda, Noby Hata)<br />
#[[2010_Summer_Project_Week_Implementing_OpenCV_to_Slicer3_for_Neuroendoscopic_Surgery|Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery]] (Atsushi Yamada, Junichi Tokuda, 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 />
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnotta, Peter Karasev, Curt Lisle, Ron Kikinis) <br />
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)<br />
#[[2010_Summer_Project_Week_Mouse_Brain_Cortical_Thickness_Analysis|Mouse brain cortical thickness analysis]] (Joohwi Lee, Ipek Oguz, Martin Styner)<br />
#[[2010_Summer_Project_Week_Primate image analysis using the standard Slicer pipeline|Primate image analysis using the standard Slicer pipeline]] (Yundi Shi, 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 />
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)<br />
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)<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, Raghav Padmanabhan, Arnaud Gelas, Sean Megason, Badri Roysam)<br />
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Kishore Mosaliganti, Arnaud Gelas, Sean Megason, Raghu Machiraju)<br />
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)<br />
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Arnaud Gelas, Stever Pieper)<br />
# [[Seedings results comparison]] (Antonin Perrot-Audet, Raghav Padmanabhan, 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 />
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)<br />
<br />
=== Shape Analysis ===<br />
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)<br />
# [[2010_Summer_Project_Week_Shape_Analysis_UNC|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 />
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)<br />
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)<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 />
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)<br />
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, 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, Jim Barabas)<br />
#[[2010 NAMIC Project week:Inventory of Volume Rendering Functionality|Inventory of Volume Rendering Functionality]] (Jim Barabas)<br />
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)<br />
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)<br />
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)<br />
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)<br />
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]](David Partyka, Steve Pieper, Katie Hayes)<br />
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)<br />
#[[2010 NAMIC Project week: Volume Rendering for Virtual Colonoscopy|Volume Rendering for Virtual Colonoscopy]] (Hiro Yoshida, Yin Wu, Steve Piper, Ron Kikinis)<br />
<br />
=== Workflows and Integration ===<br />
# [[Summer_project_week_2010_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)<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 />
<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 />
# Yousef Al-Kofahi , CompuCyte Corporation<br />
# Peter Anderson , retired<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 />
# Randy Gollub , MGH<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 />
# Joohwi Lee , UNC Chapel Hill<br />
# Rui Li , MGH<br />
# Stefan Lienhard , LMI<br />
# Curtis Lisle , KnowledgeVis, LLC<br />
# Haiying Liu , Brigham and Women's Hospital<br />
# Felix Liu , Beth Israel Deaconess Medical Center<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 />
# William Marks , Focused Ultrasound Lab, BWH, HMS<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 />
# Beck Olson , UCSF<br />
# John Onofrey , Yale University<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 />
# Eun-Joo Park , Brigham & Women's Hospital<br />
# David Partyka , Kitware Inc<br />
# Pratik Patel , <br />
# Sudhir Pathak , Univeristy Of Pittsburgh<br />
# Thierry PECOT , Ohio State University<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 />
# Johannes Schick , SPL<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 />
# Matthew Toews , Brigham and Women's Hospital, Harvard Medical School<br />
# Junichi Tokuda , Brigham and Women's Hospital<br />
# Tamas Ungi , Queen's University<br />
# Clement Vachet , UNC Chapel Hill<br />
# Veda Vadyar , Brigham and Women's Hospital<br />
# Gopalkrishna Veni , SCI Institute<br />
# Stuart Wallace , Massachusetts General Hospital<br />
# Demian Wassermann , SPL/LMI/PNL<br />
# Adam Weinrich , Nokia<br />
# Sandy Wells , BWH<br />
# Phillip White , BWH/HMS<br />
# Guorong Wu , University of North Carolina at Chapel Hill<br />
# Yin Wu , Mass General Hospital<br />
# Atsushi Yamada , Nagoya Institute of Technology<br />
# Alexander Yarmarkovich , ISOMICS<br />
# Alexander Zaitsev , Brigham and Womens Hospital</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Import/Export_Farsight-GoFigure_results&diff=54653Import/Export Farsight-GoFigure results2010-06-20T14:16:18Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Lydie Souhait, Arnaud Gelas, Sean Megason<br />
* RPI: Raghav Padmanabhan, Badri Roysam<br />
<br />
==Project==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Exchange data (cell segmentation results) between Farsight and Gofigure2<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Discuss current status of both projects<br />
* Define common objects/traces used by both projects<br />
* Install both projects<br />
* Export the data from both projects into textfiles<br />
* Import the data from Farsight into Gofigure Database<br />
* Import the data from Gofigure Database into Farsight<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Export Contours from Gofigure2 into textfile done<br />
* Import Contours from textfile into Gofigure2 database done<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Import/Export_Farsight-GoFigure_results&diff=54652Import/Export Farsight-GoFigure results2010-06-20T14:14:36Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Lydie Souhait, Arnaud Gelas, Sean Megason<br />
* RPI: Raghav Padmanabhan, Badri Roysam<br />
<br />
==Project==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Exchange data (cell segmentation results) between Farsight and Gofigure2<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Discuss current status of both projects<br />
* Define common objects/traces used by both projects<br />
* Export the data from both projects into textfiles<br />
* Import the data from Farsight into Gofigure Database<br />
* Find a way to import the data from Gofigure into Farsight<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Export Contours from Gofigure2 into textfile done<br />
* Import Contours from textfile into Gofigure2 database done<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week&diff=546512010 Summer Project Week2010-06-20T14:14:16Z<p>Arnaudgelas: /* Microscopy Image Analysis */</p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
<br />
[[Image:PW-MIT2010.png|500px|right]]<br />
<br />
__TOC__<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background: #b0d5e6; color: #02186f; font-size: 130%" <br />
!Time<br />
!width="250px"|Monday, June 21<br />
!width="250px"|Tuesday, June 22<br />
!width="250px"|Wednesday, June 23<br />
!width="250px"|Thursday, June 24<br />
!width="250px"|Friday, June 25<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''9am:''' NA-MIC Kit Update (Jim Miller) <br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''9:45am:''' [[Media:2010_Project_Week_Slicer.ppt|3D Slicer Update]] (Steve Pieper)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''10:30-11am:''' OpenIGTLink Update (Junichi Tokuda)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''11am-12pm:''' Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room A]]<br />
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)<br />
|'''9am-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-5:30pm: Tutorial:''' [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)<br />
<br>[[MIT_Project_Week_Rooms#32-155|32-155 (Stata Lecture Hall)]]<br />
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> QT/Slicer (Steve, JC, J2)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
<br>----------------------------------------<br><br />
'''3-4pm:''' [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''4-5pm: <font color="#4020ff">Breakout Session:'''</font><br />
<br> [[2010 Summer Project Week Breakout Session: Data Management |Data Management]] (Dan Marcus, Stephen Aylward)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
|'''12:45-1pm:''' [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]<br />
<br>----------------------------------------<br><br />
'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)<br />
<br>----------------------------------------<br><br />
'''3-5pm: <font color="#4020ff">Breakout Session:'''</font><br><br />
[[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)<br />
<br>----------------------------------------<br><br />
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widgets]] (Nicole, Kilian, JC)<br />
|'''1-2pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)<br />
<br>----------------------------------------<br><br />
'''2-3pm:''' Build Instructions: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)<br />
<br>----------------------------------------<br><br />
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> <br />
[[2010 Summer Project Week Breakout Session: Volume Rendering|Volume Rendering Demos and Discussion]] (Yin Wu, Steve Pieper)<br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
<br />
Please note:<br />
*We need to empty room by 1:30pm on Friday. 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| January 3-7, 2011, Salt Lake City, 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, Andriy Fedorov)<br />
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)<br />
<br />
=== IGT ===<br />
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)<br />
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)<br />
#[[2010_Summer_Project_Week_Prostate_Intervention|Prostate Intervention(Junichi, Sam Song, Tamas Ungi)]]<br />
#[[2010_Summer_Project_Week_Liver_Ablation|Liver Ablation (Haiying Liu, Noby Hata)]]<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 />
#[[2010_Summer_Project_Week_Tracking_Neuroendoscope_Using_EM_Tracker_and_OpenIGTLink|Tracking Neuroendoscope Using EM Tracker and OpenIGTLink]] (Laurent Chauvin, Junichi Tokuda, Noby Hata)<br />
#[[2010_Summer_Project_Week_Implementing_OpenCV_to_Slicer3_for_Neuroendoscopic_Surgery|Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery]] (Atsushi Yamada, Junichi Tokuda, 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 />
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnotta, Peter Karasev, Curt Lisle, Ron Kikinis) <br />
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)<br />
#[[2010_Summer_Project_Week_Mouse_Brain_Cortical_Thickness_Analysis|Mouse brain cortical thickness analysis]] (Joohwi Lee, Ipek Oguz, Martin Styner)<br />
#[[2010_Summer_Project_Week_Primate image analysis using the standard Slicer pipeline|Primate image analysis using the standard Slicer pipeline]] (Yundi Shi, 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 />
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)<br />
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)<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, Raghav Padmanabhan, Arnaud Gelas, Sean Megason, Badri Roysam)<br />
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Kishore Mosaliganti, Arnaud Gelas, Sean Megason, Raghu Machiraju)<br />
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)<br />
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Arnaud Gelas, 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 />
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)<br />
<br />
=== Shape Analysis ===<br />
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)<br />
# [[2010_Summer_Project_Week_Shape_Analysis_UNC|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 />
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)<br />
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)<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 />
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)<br />
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, 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, Jim Barabas)<br />
#[[2010 NAMIC Project week:Inventory of Volume Rendering Functionality|Inventory of Volume Rendering Functionality]] (Jim Barabas)<br />
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)<br />
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)<br />
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)<br />
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)<br />
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]](David Partyka, Steve Pieper, Katie Hayes)<br />
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)<br />
#[[2010 NAMIC Project week: Volume Rendering for Virtual Colonoscopy|Volume Rendering for Virtual Colonoscopy]] (Hiro Yoshida, Yin Wu, Steve Piper, Ron Kikinis)<br />
<br />
=== Workflows and Integration ===<br />
# [[Summer_project_week_2010_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)<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 />
<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 />
# Yousef Al-Kofahi , CompuCyte Corporation<br />
# Peter Anderson , retired<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 />
# Randy Gollub , MGH<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 />
# Joohwi Lee , UNC Chapel Hill<br />
# Rui Li , MGH<br />
# Stefan Lienhard , LMI<br />
# Curtis Lisle , KnowledgeVis, LLC<br />
# Haiying Liu , Brigham and Women's Hospital<br />
# Felix Liu , Beth Israel Deaconess Medical Center<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 />
# William Marks , Focused Ultrasound Lab, BWH, HMS<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 />
# Beck Olson , UCSF<br />
# John Onofrey , Yale University<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 />
# Eun-Joo Park , Brigham & Women's Hospital<br />
# David Partyka , Kitware Inc<br />
# Pratik Patel , <br />
# Sudhir Pathak , Univeristy Of Pittsburgh<br />
# Thierry PECOT , Ohio State University<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 />
# Johannes Schick , SPL<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 />
# Matthew Toews , Brigham and Women's Hospital, Harvard Medical School<br />
# Junichi Tokuda , Brigham and Women's Hospital<br />
# Tamas Ungi , Queen's University<br />
# Clement Vachet , UNC Chapel Hill<br />
# Veda Vadyar , Brigham and Women's Hospital<br />
# Gopalkrishna Veni , SCI Institute<br />
# Stuart Wallace , Massachusetts General Hospital<br />
# Demian Wassermann , SPL/LMI/PNL<br />
# Adam Weinrich , Nokia<br />
# Sandy Wells , BWH<br />
# Phillip White , BWH/HMS<br />
# Guorong Wu , University of North Carolina at Chapel Hill<br />
# Yin Wu , Mass General Hospital<br />
# Atsushi Yamada , Nagoya Institute of Technology<br />
# Alexander Yarmarkovich , ISOMICS<br />
# Alexander Zaitsev , Brigham and Womens Hospital</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week&diff=546502010 Summer Project Week2010-06-20T14:11:32Z<p>Arnaudgelas: /* Microscopy Image Analysis */</p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
<br />
[[Image:PW-MIT2010.png|500px|right]]<br />
<br />
__TOC__<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background: #b0d5e6; color: #02186f; font-size: 130%" <br />
!Time<br />
!width="250px"|Monday, June 21<br />
!width="250px"|Tuesday, June 22<br />
!width="250px"|Wednesday, June 23<br />
!width="250px"|Thursday, June 24<br />
!width="250px"|Friday, June 25<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''9am:''' NA-MIC Kit Update (Jim Miller) <br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''9:45am:''' [[Media:2010_Project_Week_Slicer.ppt|3D Slicer Update]] (Steve Pieper)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''10:30-11am:''' OpenIGTLink Update (Junichi Tokuda)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''11am-12pm:''' Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room A]]<br />
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)<br />
|'''9am-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-5:30pm: Tutorial:''' [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)<br />
<br>[[MIT_Project_Week_Rooms#32-155|32-155 (Stata Lecture Hall)]]<br />
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> QT/Slicer (Steve, JC, J2)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
<br>----------------------------------------<br><br />
'''3-4pm:''' [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''4-5pm: <font color="#4020ff">Breakout Session:'''</font><br />
<br> [[2010 Summer Project Week Breakout Session: Data Management |Data Management]] (Dan Marcus, Stephen Aylward)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
|'''12:45-1pm:''' [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]<br />
<br>----------------------------------------<br><br />
'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)<br />
<br>----------------------------------------<br><br />
'''3-5pm: <font color="#4020ff">Breakout Session:'''</font><br><br />
[[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)<br />
<br>----------------------------------------<br><br />
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widgets]] (Nicole, Kilian, JC)<br />
|'''1-2pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)<br />
<br>----------------------------------------<br><br />
'''2-3pm:''' Build Instructions: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)<br />
<br>----------------------------------------<br><br />
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> <br />
[[2010 Summer Project Week Breakout Session: Volume Rendering|Volume Rendering Demos and Discussion]] (Yin Wu, Steve Pieper)<br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
<br />
Please note:<br />
*We need to empty room by 1:30pm on Friday. 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| January 3-7, 2011, Salt Lake City, 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, Andriy Fedorov)<br />
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)<br />
<br />
=== IGT ===<br />
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)<br />
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)<br />
#[[2010_Summer_Project_Week_Prostate_Intervention|Prostate Intervention(Junichi, Sam Song, Tamas Ungi)]]<br />
#[[2010_Summer_Project_Week_Liver_Ablation|Liver Ablation (Haiying Liu, Noby Hata)]]<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 />
#[[2010_Summer_Project_Week_Tracking_Neuroendoscope_Using_EM_Tracker_and_OpenIGTLink|Tracking Neuroendoscope Using EM Tracker and OpenIGTLink]] (Laurent Chauvin, Junichi Tokuda, Noby Hata)<br />
#[[2010_Summer_Project_Week_Implementing_OpenCV_to_Slicer3_for_Neuroendoscopic_Surgery|Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery]] (Atsushi Yamada, Junichi Tokuda, 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 />
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnotta, Peter Karasev, Curt Lisle, Ron Kikinis) <br />
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)<br />
#[[2010_Summer_Project_Week_Mouse_Brain_Cortical_Thickness_Analysis|Mouse brain cortical thickness analysis]] (Joohwi Lee, Ipek Oguz, Martin Styner)<br />
#[[2010_Summer_Project_Week_Primate image analysis using the standard Slicer pipeline|Primate image analysis using the standard Slicer pipeline]] (Yundi Shi, 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 />
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)<br />
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)<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, Kishore Mosaliganti, Arnaud Gelas, Sean Megason, Raghu Machiraju)<br />
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)<br />
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Arnaud Gelas, 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 />
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)<br />
<br />
=== Shape Analysis ===<br />
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)<br />
# [[2010_Summer_Project_Week_Shape_Analysis_UNC|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 />
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)<br />
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)<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 />
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)<br />
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, 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, Jim Barabas)<br />
#[[2010 NAMIC Project week:Inventory of Volume Rendering Functionality|Inventory of Volume Rendering Functionality]] (Jim Barabas)<br />
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)<br />
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)<br />
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)<br />
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)<br />
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]](David Partyka, Steve Pieper, Katie Hayes)<br />
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)<br />
#[[2010 NAMIC Project week: Volume Rendering for Virtual Colonoscopy|Volume Rendering for Virtual Colonoscopy]] (Hiro Yoshida, Yin Wu, Steve Piper, Ron Kikinis)<br />
<br />
=== Workflows and Integration ===<br />
# [[Summer_project_week_2010_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)<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 />
<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 />
# Yousef Al-Kofahi , CompuCyte Corporation<br />
# Peter Anderson , retired<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 />
# Randy Gollub , MGH<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 />
# Joohwi Lee , UNC Chapel Hill<br />
# Rui Li , MGH<br />
# Stefan Lienhard , LMI<br />
# Curtis Lisle , KnowledgeVis, LLC<br />
# Haiying Liu , Brigham and Women's Hospital<br />
# Felix Liu , Beth Israel Deaconess Medical Center<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 />
# William Marks , Focused Ultrasound Lab, BWH, HMS<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 />
# Beck Olson , UCSF<br />
# John Onofrey , Yale University<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 />
# Eun-Joo Park , Brigham & Women's Hospital<br />
# David Partyka , Kitware Inc<br />
# Pratik Patel , <br />
# Sudhir Pathak , Univeristy Of Pittsburgh<br />
# Thierry PECOT , Ohio State University<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 />
# Johannes Schick , SPL<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 />
# Matthew Toews , Brigham and Women's Hospital, Harvard Medical School<br />
# Junichi Tokuda , Brigham and Women's Hospital<br />
# Tamas Ungi , Queen's University<br />
# Clement Vachet , UNC Chapel Hill<br />
# Veda Vadyar , Brigham and Women's Hospital<br />
# Gopalkrishna Veni , SCI Institute<br />
# Stuart Wallace , Massachusetts General Hospital<br />
# Demian Wassermann , SPL/LMI/PNL<br />
# Adam Weinrich , Nokia<br />
# Sandy Wells , BWH<br />
# Phillip White , BWH/HMS<br />
# Guorong Wu , University of North Carolina at Chapel Hill<br />
# Yin Wu , Mass General Hospital<br />
# Atsushi Yamada , Nagoya Institute of Technology<br />
# Alexander Yarmarkovich , ISOMICS<br />
# Alexander Zaitsev , Brigham and Womens Hospital</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=CTK_Transfer_function_widget&diff=54649CTK Transfer function widget2010-06-20T14:09:58Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Nicolas Rannou, Arnaud Gelas<br />
* Kitware: Julien Finet<br />
* Isomics: Steve Pieper<br />
<br />
==Project==<br />
<br />
[[File:CtkVTKPiecewiseFunction.png|400px]] [[File:Megasonlab multichannel.png|350px]]<br />
<br />
<div style="margin: 10px;"><br />
<div style="width: 50%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Enhance the [http://www.commontk.org/index.php/Documentation/ctkTransferFunctionWidget CTK Transfer Function Widgets]<br />
* Improve design/structure of the widget<br />
* Integrate it in [http://gofigure2.sourceforge.net/ GoFigure2] ( [http://sourceforge.net/apps/trac/gofigure2/wiki Wiki page] ) for multichannel images visualization<br />
* Source code<br />
CTK GIT: git@github.com:commontk/CTK.git<br />
<br />
GoFigure2 SVN: https://gofigure2.svn.sourceforge.net/svnroot/gofigure2 <br />
* Datasets<br />
[[File:Datasets.zip]]<br />
<br />
</div><br />
<div style="width: 25%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Discuss with Julien, Ron, Sean, Steve and Arnaud about the needs, structure, etc.<br />
* Get the CTK color and piecewise transfer functions working<br />
* The transfer functions background should be the image of interest's histogram<br />
* Implement the color transfer function widget in GoFigure2 to visualize multichannel images<br />
<br />
</div><br />
<div style="width: 18%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week_Breakout_Session:_Volume_Rendering&diff=545572010 Summer Project Week Breakout Session: Volume Rendering2010-06-18T14:21:06Z<p>Arnaudgelas: </p>
<hr />
<div>[[2010_Summer_Project_Week|Back to Project Week 2010]]<br />
<br />
= Breakout session on Volume Rendering =<br />
Goal of this session is to compare and contrast various volume rendering approaches in the context of clinical application scenarios. This will mainly be done through hands-on demos and group discussion.<br />
<br />
* When: 3pm Thursday June 24<br />
* Where: at a projector in the project week room.<br />
<br />
Systems to examine:<br />
* VTK GPU Raycasting in slicer 3.6 (GLSL)<br />
* NCI GPU Raycasting in slicer 3.6 (GLSL)<br />
* Microsoft research volume rendering demo (CUDA, closed source)<br />
* Others?<br />
<br />
Scenarios:<br />
* Virtual Colonoscopy<br />
* PET-CT<br />
* Microscopy<br />
<br />
== Preparation ==<br />
Earlier in the project week we will work on getting the same datasets loaded on the various systems.<br />
<br />
== Participants ==<br />
Please add your name to the list if you are interested in participating in this session<br />
# Steve Pieper, Isomics, Inc.<br />
# Julien Finet, Kitware Inc.<br />
# Alex Yarmarkovich, Isomics, Inc.<br />
# Yanling Liu, SAIC-Frederick/NCI-Frederick.<br />
# Jim Barabas, MIT Media Lab.<br />
# Arnaud Gelas, Harvard Medical School</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=CTK_Transfer_function_widget&diff=53820CTK Transfer function widget2010-06-14T19:39:46Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Nicolas Rannou<br />
* Kitware: Julien Finet<br />
* Isomics: Steve Pieper<br />
<br />
==Project==<br />
<br />
[[File:CtkVTKPiecewiseFunction.png|400px]] [[File:Megasonlab multichannel.png|350px]]<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Enhance the [http://www.commontk.org/index.php/Documentation/ctkTransferFunctionWidget CTK Transfer Function Widgets]<br />
* Improve design/structure of the widget<br />
* Integrate it in GoFigure2<br />
* Datasets<br />
[[File:Datasets.zip]]<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Discuss with Ron, Sean, Steve, Julien and Arnaud about the needs, structure, etc.<br />
* Add a color transfer function widget in GoFigure2<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>Arnaudgelashttps://www.na-mic.org/w/index.php?title=CTK_Transfer_function_widget&diff=53819CTK Transfer function widget2010-06-14T19:37:51Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Nicolas Rannou<br />
* Kitware: Julien Finet<br />
* Isomics: Steve Pieper<br />
<br />
==Project==<br />
<br />
[[File:CtkVTKPiecewiseFunction.png|400px]] [[File:Megasonlab multichannel.png|350px]]<br />
<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Enhance the [http://www.commontk.org/index.php/Documentation/ctkTransferFunctionWidget CTK Transfer Function Widgets]<br />
* Improve design/structure of the widget<br />
* Integrate it in GoFigure2<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Discuss with Ron, Sean, Steve, Julien and Arnaud about the needs, structure, etc.<br />
* Add a color transfer function widget in GoFigure2<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>Arnaudgelashttps://www.na-mic.org/w/index.php?title=File:Megasonlab_multichannel.png&diff=53818File:Megasonlab multichannel.png2010-06-14T19:34:50Z<p>Arnaudgelas: Megasonlab_multichannel.png</p>
<hr />
<div>Megasonlab_multichannel.png</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=File:Megasonlab_multichannel.tif&diff=53817File:Megasonlab multichannel.tif2010-06-14T19:32:48Z<p>Arnaudgelas: Megasonlab_multichannel.tif</p>
<hr />
<div>Megasonlab_multichannel.tif</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=File:Datasets.zip&diff=53814File:Datasets.zip2010-06-14T19:27:07Z<p>Arnaudgelas: Provided by the Megason Laboratory (https://wiki.med.harvard.edu/SysBio/Megason/WebHome) for NAMIC Summer Project Week in Boston (June 2010). Multichannels images</p>
<hr />
<div>Provided by the Megason Laboratory (https://wiki.med.harvard.edu/SysBio/Megason/WebHome) for NAMIC Summer Project Week in Boston (June 2010). Multichannels images</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Farsight_nuclear_segmentation_as_GoFigure_plugin&diff=53583Farsight nuclear segmentation as GoFigure plugin2010-06-09T19:53:42Z<p>Arnaudgelas: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
Image:Hippocampus.jpg|Farsight nuclei segmentation<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Harvard Medical School: Arnaud Gelas, Sean Megason<br />
* RPI: Badri Roysam<br />
<br />
== Project ==<br />
<br />
* GoFigure2 http://gofigure2.sourceforge.net<br />
GoFigure2 is a software <br />
<br />
* Farsight http://www.farsight-toolkit.org/wiki/Main_Page<br />
Farsight project is Developing Quantitative Tools for Studying Complex and Dynamic Biological Micro-environments from 4D/5D Microscopy Data<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
<br />
* Enable GoFigure2 plugin mechanism<br />
* Develop one GoFigure2's plugin from Farsight nuclear segmentation<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
* Make a simple Image To Image plugin work into GoFigure2<br />
* Download, build and install farsight<br />
* Run Farsight nuclear segmentation as an executable<br />
** Import results into GoFigure2 (see previous project)<br />
* Make a plugin from this application<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
* GoFigure2's Image to Image plugins can be <br />
** compiled<br />
** loaded<br />
** ran<br />
* There is one bug when importing back the results of the plugin into GoFigure<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=File:Hippocampus.jpg&diff=53582File:Hippocampus.jpg2010-06-09T19:52:59Z<p>Arnaudgelas: uploaded a new version of "File:Hippocampus.jpg"</p>
<hr />
<div>One application of FARSIGHT is to map the structure of complex tissues</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Farsight_nuclear_segmentation_as_GoFigure_plugin&diff=53581Farsight nuclear segmentation as GoFigure plugin2010-06-09T19:50:02Z<p>Arnaudgelas: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
Image:Hippocampus.jpg|Farsight<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Harvard Medical School: Arnaud Gelas, Sean Megason<br />
* RPI: Badri Roysam<br />
<br />
== Project ==<br />
<br />
* GoFigure2 http://gofigure2.sourceforge.net<br />
GoFigure2 is a software <br />
<br />
* Farsight http://www.farsight-toolkit.org/wiki/Main_Page<br />
Farsight project is Developing Quantitative Tools for Studying Complex and Dynamic Biological Micro-environments from 4D/5D Microscopy Data<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
<br />
* Enable GoFigure2 plugin mechanism<br />
* Develop one GoFigure2's plugin from Farsight nuclear segmentation<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
* Make a simple Image To Image plugin work into GoFigure2<br />
* Download, build and install farsight<br />
* Run Farsight nuclear segmentation as an executable<br />
** Import results into GoFigure2 (see previous project)<br />
* Make a plugin from this application<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
* GoFigure2's Image to Image plugins can be <br />
** compiled<br />
** loaded<br />
** ran<br />
* There is one bug when importing back the results of the plugin into GoFigure<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=File:Hippocampus.jpg&diff=53580File:Hippocampus.jpg2010-06-09T19:48:54Z<p>Arnaudgelas: One application of FARSIGHT is to map the structure of complex tissues</p>
<hr />
<div>One application of FARSIGHT is to map the structure of complex tissues</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Farsight_nuclear_segmentation_as_GoFigure_plugin&diff=53579Farsight nuclear segmentation as GoFigure plugin2010-06-09T19:46:45Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Arnaud Gelas, Sean Megason<br />
* RPI: Badri Roysam<br />
<br />
== Project ==<br />
<br />
* GoFigure2 http://gofigure2.sourceforge.net<br />
GoFigure2 is a software <br />
<br />
* Farsight http://www.farsight-toolkit.org/wiki/Main_Page<br />
Farsight project is Developing Quantitative Tools for Studying Complex and Dynamic Biological Micro-environments from 4D/5D Microscopy Data<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
<br />
* Enable GoFigure2 plugin mechanism<br />
* Develop one GoFigure2's plugin from Farsight nuclear segmentation<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
* Make a simple Image To Image plugin work into GoFigure2<br />
* Download, build and install farsight<br />
* Run Farsight nuclear segmentation as an executable<br />
** Import results into GoFigure2 (see previous project)<br />
* Make a plugin from this application<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
* GoFigure2's Image to Image plugins can be <br />
** compiled<br />
** loaded<br />
** ran<br />
* There is one bug when importing back the results of the plugin into GoFigure<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Farsight_nuclear_segmentation_as_GoFigure_plugin&diff=53578Farsight nuclear segmentation as GoFigure plugin2010-06-09T19:42:43Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Arnaud Gelas, Sean Megason<br />
* RPI: Badri Roysam<br />
<br />
== Project ==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
<br />
* Enable GoFigure2 plugin mechanism<br />
* Develop one GoFigure2's plugin from Farsight nuclear segmentation<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
* Make a simple Image To Image plugin work into GoFigure2<br />
* Download, build and install farsight<br />
* Run Farsight nuclear segmentation as an executable<br />
** Import results into GoFigure2 (see previous project)<br />
* Make a plugin from this application<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
* GoFigure2's Image to Image plugins can be <br />
** compiled<br />
** loaded<br />
** ran<br />
* There is one bug when importing back the results of the plugin into GoFigure<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Import/Export_Farsight-GoFigure_results&diff=53573Import/Export Farsight-GoFigure results2010-06-09T13:38:23Z<p>Arnaudgelas: </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 />
* Harvard Medical School: Lydie Souhait, Arnaud Gelas, Sean Megason<br />
* RPI: Badri Roysam<br />
<br />
==Project==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Exchange data (cell segmentation results) between Farsight and Gofigure2<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Discuss current status of both projects<br />
* Define common objects/traces used by both projects<br />
* Export the data from both projects into textfiles<br />
* Import the data from Farsight into Gofigure Database<br />
* Find a way to import the data from Gofigure into Farsight<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Export Contours from Gofigure2 into textfile done<br />
* Import Contours from textfile into Gofigure2 database done<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Import/Export_Farsight-GoFigure_results&diff=53572Import/Export Farsight-GoFigure results2010-06-09T13:36:27Z<p>Arnaudgelas: </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 />
* Harvard Medical School: Lydie Souhait, Arnaud Gelas, Sean Megason<br />
* RPI: Badri Roysam<br />
<br />
==Project==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Exchange data (cell segmentation results) between Farsight and Gofigure2<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Discuss current status of both projects<br />
* Define common objects/traces used by both projects<br />
* Export the data from both projects into textfiles<br />
* Import the data from Farsight into Gofigure Database<br />
* Find a way to import the data from Gofigure into <br />
Farsight<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Export Contours from Gofigure2 into textfile done<br />
* Import Contours from textfile into Gofigure2 database done<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Seedings_results_comparison&diff=53507Seedings results comparison2010-06-08T22:14:43Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason<br />
* RPI: Badri Roysam<br />
<br />
==Project==<br />
[[File:Seed.png]]<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Improve segmentation algorithms initialization for nuclei detection in 3D fluorescent microscopy:<br />
** get a better accuracy,<br />
** improve computation speed.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Compare different algorithms,<br />
* Find a measure to evaluate different algorithm results,<br />
* Fusion output of several algorithms.<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Implemented 3 different algorithms with ITK:<br />
** Tensor voting,<br />
** Hough transform,<br />
** Multi-scale Distance Map weighted Laplacian of Gaussian. <br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Seedings_results_comparison&diff=53506Seedings results comparison2010-06-08T22:14:06Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason<br />
* RPI: Badri Roysam<br />
<br />
==Project==<br />
[[File:Seed.png]]<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Improve segmentation algorithms initialization for nuclei detection in 3D fluorescent microscopy:<br />
** get a better accuracy,<br />
** improve computation speed.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Compare different algorithms,<br />
* Find a measure to evaluate different algorithm results,<br />
* Fusion output of several algorithms.<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Implemented 3 different algorrithms with ITK:<br />
** Tensor voting,<br />
** Hough transform,<br />
** Multiscale Distance Map weighted Laplacian of Gaussian. <br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=File:Seed.png&diff=53505File:Seed.png2010-06-08T22:13:13Z<p>Arnaudgelas: </p>
<hr />
<div></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Seedings_results_comparison&diff=53504Seedings results comparison2010-06-08T22:12:52Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason<br />
* RPI: Badri Roysam<br />
<br />
==Project==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Improve segmentation algorithms initialization for nuclei detection in 3D fluorescent microscopy:<br />
** get a better accuracy,<br />
** improve computation speed.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Compare different algorithms,<br />
* Find a measure to evaluate different algorithm results,<br />
* Fusion output of several algorithms.<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Implemented 3 different algorrithms with ITK:<br />
** Tensor voting,<br />
** Hough transform,<br />
** Multiscale Distance Map weighted Laplacian of Gaussian. <br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=CTK_Transfer_function_widget&diff=53497CTK Transfer function widget2010-06-08T21:58:57Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Nicolas Rannou<br />
* Kitware: Julien Finet<br />
* Isomics: Steve Pieper<br />
<br />
==Project==<br />
<br />
[[File:CtkVTKPiecewiseFunction.png]]<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Enhance the [http://www.commontk.org/index.php/Documentation/ctkTransferFunctionWidget CTK Transfer Function Widgets]<br />
* Improve design/structure of the widget<br />
* Integrate it in GoFigure2<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Discuss with Ron, Sean, Steve, Julien and Arnaud about the needs, structure, etc.<br />
* Add a color transfer function widget in GoFigure2<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>Arnaudgelashttps://www.na-mic.org/w/index.php?title=File:CtkTransferFunctionWidget.png&diff=53493File:CtkTransferFunctionWidget.png2010-06-08T21:53:02Z<p>Arnaudgelas: CtkTransferFunctionWidget.png</p>
<hr />
<div>CtkTransferFunctionWidget.png</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=CTK_Transfer_function_widget&diff=53492CTK Transfer function widget2010-06-08T21:52:50Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Nicolas Rannou<br />
* Kitware: Julien Finet<br />
* Isomics: Steve Pieper<br />
<br />
==Project==<br />
<br />
[[File:CtkVTKPiecewiseFunction.png]]<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Enhance the [http://www.commontk.org/index.php/Documentation/ctkTransferFunctionWidget CTK Transfer Function Widgets]<br />
* Improve design/structure of the widget<br />
* Integrate it in GoFigure2<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Talk with Ron, Steve and Julien about needs, structure, etc.<br />
* Add a color transfer function widget in GoFigure2<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>Arnaudgelashttps://www.na-mic.org/w/index.php?title=File:CtkVTKPiecewiseFunction.png&diff=53490File:CtkVTKPiecewiseFunction.png2010-06-08T21:49:40Z<p>Arnaudgelas: CtkVTKPiecewiseFunction.png</p>
<hr />
<div>CtkVTKPiecewiseFunction.png</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=CTK_Transfer_function_widget&diff=53489CTK Transfer function widget2010-06-08T21:48:45Z<p>Arnaudgelas: /* 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 />
* Harvard Medical School: Nicolas Rannou<br />
* Kitware: Julien Finet<br />
* Isomics: Steve Pieper<br />
<br />
==Project==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
[[File:Example.jpg]]<br />
<br />
<h3>Objective</h3><br />
* Enhance the ctk transfer function widget<br />
* Improve design/structure of the widget<br />
* Integrate it in GoFigure2<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Talk with Ron, Steve and Julien about needs, structure, etc.<br />
* Add a color transfer function widget in GoFigure2<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>Arnaudgelashttps://www.na-mic.org/w/index.php?title=ITK_GPAC_level_set&diff=53318ITK GPAC level set2010-06-03T20:30:55Z<p>Arnaudgelas: </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 />
* University of Missouri: K. Palaniappan<br />
* Harvard Medical School: Kishore Mosaliganti, Sean Megason<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>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Seedings_results_comparison&diff=53317Seedings results comparison2010-06-03T20:30:34Z<p>Arnaudgelas: </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 />
* Harvard Medical School: Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason<br />
* RPI: Badri Roysam<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>Arnaudgelashttps://www.na-mic.org/w/index.php?title=CTK_Transfer_function_widget&diff=53316CTK Transfer function widget2010-06-03T20:30:13Z<p>Arnaudgelas: </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 />
* Harvard Medical School: Nicolas Rannou<br />
* Kitware: Julien Finet<br />
* Isomics: Steve Pieper<br />
<br />
==Project==<br />
<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>Arnaudgelashttps://www.na-mic.org/w/index.php?title=ITK_Spherical_Harmonics_filter_for_shape_analysis_of_cell_nuclei&diff=53314ITK Spherical Harmonics filter for shape analysis of cell nuclei2010-06-03T20:29:42Z<p>Arnaudgelas: </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 />
* OSU: Shantanu Singh, Raghu Machiraju<br />
* Harvard Medical School: Arnaud Gelas, Sean Megason<br />
<br />
==Project==<br />
<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>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Farsight_nuclear_segmentation_as_GoFigure_plugin&diff=53313Farsight nuclear segmentation as GoFigure plugin2010-06-03T20:29:02Z<p>Arnaudgelas: </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 />
* Harvard Medical School: Arnaud Gelas, Sean Megason<br />
* RPI: Badri Roysam<br />
<br />
== Project ==<br />
<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>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Import/Export_Farsight-GoFigure_results&diff=53312Import/Export Farsight-GoFigure results2010-06-03T20:28:34Z<p>Arnaudgelas: </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 />
* Harvard Medical School: Lydie Souhait, Arnaud Gelas, Sean Megason<br />
* RPI: Badri Roysam<br />
<br />
==Project==<br />
<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 />
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<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Import/Export_Farsight-GoFigure_results&diff=53311Import/Export Farsight-GoFigure results2010-06-03T20:24:24Z<p>Arnaudgelas: /* Key Investigators */</p>
<hr />
<div>==Key Investigators==<br />
* Harvard Medical School: Lydie Souhait, Arnaud Gelas, Sean Megason<br />
* RPI: Badri Roysam<br />
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==Project==<br />
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<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Seedings_results_comparison&diff=53310Seedings results comparison2010-06-03T20:23:18Z<p>Arnaudgelas: /* Key Investigators */</p>
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<div>==Key Investigators==<br />
* Harvard Medical School: Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason<br />
* RPI: Badri Roysam<br />
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<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Seedings_results_comparison&diff=53309Seedings results comparison2010-06-03T20:22:38Z<p>Arnaudgelas: Created page with '==Key Investigators== * Harvard Medical School: Nicolas Rannou * Kitware: Julien Finet * Isomics: Steve Pieper <div style="margin: 20px;"> <div style="width: 27%; float: left; p…'</p>
<hr />
<div>==Key Investigators==<br />
* Harvard Medical School: Nicolas Rannou<br />
* Kitware: Julien Finet<br />
* Isomics: Steve Pieper<br />
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<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week&diff=533082010 Summer Project Week2010-06-03T20:22:26Z<p>Arnaudgelas: /* 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 Ibanesz)<br />
**3-4pm: 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, Fill in Dates]]<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/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 />
<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)<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 Meir, Hans Johnson)<br />
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)<br />
* Liver Ablation (Haiying Liu)<br />
* BrainLab-Aurora HybridNav (Isaiah Norton, Dan Marcus)<br />
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)<br />
<br />
=== Radiotherapy ===<br />
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp)<br />
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)<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 />
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)<br />
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)<br />
<br />
===[[Microscopy Image Analysis]] ===<br />
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard<br />
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more<br />
* Gouaillard: Flow Cytometry<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, Sean Megason, Badri Roysam)<br />
* [[ITK GPAC level set]] (K. Palaniappan, Kishore Mosaliganti, Sean Megason)<br />
<br />
=== Shape Analysis ===<br />
* Median Shape by Boundary-based Distance (Tammy Riklin Raviv, Sylvain Bouix)<br />
=== Informatics ===<br />
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)<br />
<br />
=== Diffusion ===<br />
*Fluid Mechanics Based Tractography (Nathan Hageman)<br />
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)<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 />
*XNAT Enterprise webservices client for Slicer (Wendy, Mark)<br />
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)<br />
<br />
*VTKWidgets (JC, will, Schroeder, Nicole, Ron)<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 />
#Aucoin, Nicole, BWH<br />
#Audette, Michel, Kitware<br />
#Aylward, Stephen, Kitware, Inc<br />
#Boucharin, Alexis, UNC Neuro Image Research and Analysis Laboratories<br />
#Bouix, Sylvain, BWH<br />
#Budin, Francois, UNC<br />
#Burdette, Everette, Acoustic MedSystems, Inc.<br />
#Chen, Min, Johns Hopkins University<br />
#Datar, Manasi, SCI Institute<br />
#Eckbo, Ryan, BWH<br />
#Fedorov, Andriy, Surgical Planning Lab<br />
#Fillion-Robin, Jean-Christophe, Kitware Inc.<br />
#Finet, Julien, Kitware Inc<br />
#Fishbaugh, James, SCI Institute<br />
#Gao, Yi, Gerogia Tech<br />
#GELAS, Arnaud, Harvard Medical School<br />
#gouaillard, alexandre, CoSMo Software<br />
#Gouttard, Sylvain, SCI Institute<br />
#Haehn, Daniel, University of Pennsylvania<br />
#Hageman, Nathan <br />
#Hahn, Dieter, University Erlangen<br />
#Hamel, Corentin, UNC Chapel Hill<br />
#Hata, Nobuhiko, Brigham and Women's Hospital<br />
#Hayes, Kathryn, Brigham and Women's Hospital<br />
#Holton, Leslie, Medtronic Navigation<br />
#Ibanez, Luis, KITWARE Inc.<br />
#Johnson, Hans, University of Iowa<br />
#Kapur, Tina, Brigham and Women's Hospital<br />
#Kikinis, Ron, Brigham and Women's Hospital<br />
#Kim, Minjeong, UNC-Chapel Hill<br />
#Kolesov, Ivan, Georgia Institute of Technology<br />
#Larson, Garrett, UNC-CH<br />
#Li, Rui, MGH<br />
#Lisle, Curtis, KnowledgeVis, LLC<br />
#Liu, Haiying, Brigham and Women's Hospital<br />
#Liu, Yanling, SAIC-Frederick, Inc.<br />
#Magnotta, Vincent, The University of Iowa<br />
#malaterre, mathieu, CoSMo Software<br />
#Mastrogiacomo, Katie, Brigham and Women's Hospital<br />
#Matsui, Joy, University<br />
#Megason, Sean, Harvard Medical School<br />
#Meier, Dominik, BWH, Boston MA<br />
#menze, bjoern, CSAIL MIT<br />
#Mosaliganti, Kishore, Harvard Medical School<br />
#Niethammer, Marc, UNC Chapel Hill<br />
#Norton, Isaiah, BWH Neurosurgery<br />
#Paniagua, Beatriz, University of North Caolina at Chapel Hill<br />
#Papademetris, Xenophon, Yale University<br />
#Partyka, David, Kitware Inc<br />
#Pathak, Sudhir, Univeristy Of Pittsburgh<br />
#Peroni, Marta, Politecnico di Milano<br />
#Perrot-Audet, Antonin, Harvard Medical School<br />
#Pieper, Steve, Isomics, Inc.<br />
#Plesniak, Wendy, BWH<br />
#Pohl, Kilian, IBM<br />
#Pujol, Sonia, Brigham and Women's Hospital<br />
#Rannou, Nicolas, Harvard Medical School<br />
#Riklin Raviv, Tammy, MIT, CSAIL<br />
#Ruiz, Marco, UCSD<br />
#Schroeder, William, Kitware<br />
#Scully, Mark, The Mind Research Network<br />
#Sharp, Greg, MGH<br />
#Shi, Yundi, UNC Chapel Hill<br />
#Shusharina, Nadya, MGH<br />
#Smith, Gareth, Wolfson Medical Imaging Centre (WMIC)<br />
#Souhait, Lydie, Harvard Medical School<br />
#Spinczyk, Dominik, Silesian University of Technology<br />
#Srinivasan, Padmapriya <br />
#Tao, Xiaodong, GE Research<br />
#Ungi, Tamas, Queen's University<br />
#Vachet, Clement, UNC Chapel Hill<br />
#Veni, Gopalkrishna, SCI Institute<br />
#Wassermann, Demian, SPL/LMI/PNL<br />
#Wells, Sandy, BWH<br />
#Wu, Guorong, University of North Carolina at Chapel Hill</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Farsight_nuclear_segmentation_as_GoFigure_plugin&diff=53307Farsight nuclear segmentation as GoFigure plugin2010-06-03T20:20:45Z<p>Arnaudgelas: Created page with '==Key Investigators== * Harvard Medical School: Arnaud Gelas, Sean Megason * RPI: Badri Roysam <div style="margin: 20px;"> <div style="width: 27%; float: left; padding-right: 3%…'</p>
<hr />
<div>==Key Investigators==<br />
* Harvard Medical School: Arnaud Gelas, Sean Megason<br />
* RPI: Badri Roysam<br />
<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>Arnaudgelashttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week&diff=533062010 Summer Project Week2010-06-03T20:20:09Z<p>Arnaudgelas: /* 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 Ibanesz)<br />
**3-4pm: 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, Fill in Dates]]<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/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 />
<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)<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 Meir, Hans Johnson)<br />
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)<br />
* Liver Ablation (Haiying Liu)<br />
* BrainLab-Aurora HybridNav (Isaiah Norton, Dan Marcus)<br />
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)<br />
<br />
=== Radiotherapy ===<br />
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp)<br />
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)<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 />
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)<br />
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)<br />
<br />
===[[Microscopy Image Analysis]] ===<br />
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard<br />
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more<br />
* Gouaillard: Flow Cytometry<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 />
* Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason, Badri Roysam: Seeding results comparison<br />
* [[ITK GPAC level set]] (K. Palaniappan, Kishore Mosaliganti, Sean Megason)<br />
<br />
=== Shape Analysis ===<br />
* Median Shape by Boundary-based Distance (Tammy Riklin Raviv, Sylvain Bouix)<br />
=== Informatics ===<br />
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)<br />
<br />
=== Diffusion ===<br />
*Fluid Mechanics Based Tractography (Nathan Hageman)<br />
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)<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 />
*XNAT Enterprise webservices client for Slicer (Wendy, Mark)<br />
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)<br />
<br />
*VTKWidgets (JC, will, Schroeder, Nicole, Ron)<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 />
#Aucoin, Nicole, BWH<br />
#Audette, Michel, Kitware<br />
#Aylward, Stephen, Kitware, Inc<br />
#Boucharin, Alexis, UNC Neuro Image Research and Analysis Laboratories<br />
#Bouix, Sylvain, BWH<br />
#Budin, Francois, UNC<br />
#Burdette, Everette, Acoustic MedSystems, Inc.<br />
#Chen, Min, Johns Hopkins University<br />
#Datar, Manasi, SCI Institute<br />
#Eckbo, Ryan, BWH<br />
#Fedorov, Andriy, Surgical Planning Lab<br />
#Fillion-Robin, Jean-Christophe, Kitware Inc.<br />
#Finet, Julien, Kitware Inc<br />
#Fishbaugh, James, SCI Institute<br />
#Gao, Yi, Gerogia Tech<br />
#GELAS, Arnaud, Harvard Medical School<br />
#gouaillard, alexandre, CoSMo Software<br />
#Gouttard, Sylvain, SCI Institute<br />
#Haehn, Daniel, University of Pennsylvania<br />
#Hageman, Nathan <br />
#Hahn, Dieter, University Erlangen<br />
#Hamel, Corentin, UNC Chapel Hill<br />
#Hata, Nobuhiko, Brigham and Women's Hospital<br />
#Hayes, Kathryn, Brigham and Women's Hospital<br />
#Holton, Leslie, Medtronic Navigation<br />
#Ibanez, Luis, KITWARE Inc.<br />
#Johnson, Hans, University of Iowa<br />
#Kapur, Tina, Brigham and Women's Hospital<br />
#Kikinis, Ron, Brigham and Women's Hospital<br />
#Kim, Minjeong, UNC-Chapel Hill<br />
#Kolesov, Ivan, Georgia Institute of Technology<br />
#Larson, Garrett, UNC-CH<br />
#Li, Rui, MGH<br />
#Lisle, Curtis, KnowledgeVis, LLC<br />
#Liu, Haiying, Brigham and Women's Hospital<br />
#Liu, Yanling, SAIC-Frederick, Inc.<br />
#Magnotta, Vincent, The University of Iowa<br />
#malaterre, mathieu, CoSMo Software<br />
#Mastrogiacomo, Katie, Brigham and Women's Hospital<br />
#Matsui, Joy, University<br />
#Megason, Sean, Harvard Medical School<br />
#Meier, Dominik, BWH, Boston MA<br />
#menze, bjoern, CSAIL MIT<br />
#Mosaliganti, Kishore, Harvard Medical School<br />
#Niethammer, Marc, UNC Chapel Hill<br />
#Norton, Isaiah, BWH Neurosurgery<br />
#Paniagua, Beatriz, University of North Caolina at Chapel Hill<br />
#Papademetris, Xenophon, Yale University<br />
#Partyka, David, Kitware Inc<br />
#Pathak, Sudhir, Univeristy Of Pittsburgh<br />
#Peroni, Marta, Politecnico di Milano<br />
#Perrot-Audet, Antonin, Harvard Medical School<br />
#Pieper, Steve, Isomics, Inc.<br />
#Plesniak, Wendy, BWH<br />
#Pohl, Kilian, IBM<br />
#Pujol, Sonia, Brigham and Women's Hospital<br />
#Rannou, Nicolas, Harvard Medical School<br />
#Riklin Raviv, Tammy, MIT, CSAIL<br />
#Ruiz, Marco, UCSD<br />
#Schroeder, William, Kitware<br />
#Scully, Mark, The Mind Research Network<br />
#Sharp, Greg, MGH<br />
#Shi, Yundi, UNC Chapel Hill<br />
#Shusharina, Nadya, MGH<br />
#Smith, Gareth, Wolfson Medical Imaging Centre (WMIC)<br />
#Souhait, Lydie, Harvard Medical School<br />
#Spinczyk, Dominik, Silesian University of Technology<br />
#Srinivasan, Padmapriya <br />
#Tao, Xiaodong, GE Research<br />
#Ungi, Tamas, Queen's University<br />
#Vachet, Clement, UNC Chapel Hill<br />
#Veni, Gopalkrishna, SCI Institute<br />
#Wassermann, Demian, SPL/LMI/PNL<br />
#Wells, Sandy, BWH<br />
#Wu, Guorong, University of North Carolina at Chapel Hill</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=Import/Export_Farsight-GoFigure_results&diff=53305Import/Export Farsight-GoFigure results2010-06-03T20:17:09Z<p>Arnaudgelas: Created page with '==Key Investigators== * Harvard Medical School: Lydie Souhait, Arnaud Gelas, Sean Megason * RPI: Badri Roysam <div style="margin: 20px;"> <div style="width: 27%; float: left; pa…'</p>
<hr />
<div>==Key Investigators==<br />
* Harvard Medical School: Lydie Souhait, Arnaud Gelas, Sean Megason<br />
* RPI: Badri Roysam<br />
<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 />
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<h3>Approach, Plan</h3><br />
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<h3>Progress</h3><br />
<br />
</div><br />
</div><br />
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<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=ITK_GPAC_level_set&diff=53304ITK GPAC level set2010-06-03T20:16:17Z<p>Arnaudgelas: /* Key Investigators */</p>
<hr />
<div>==Key Investigators==<br />
* University of Missouri: K. Palaniappan<br />
* Harvard Medical School: Kishore Mosaliganti, Sean Megason<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
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</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
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<h3>Approach, Plan</h3><br />
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</div><br />
<div style="width: 40%; float: left;"><br />
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<h3>Progress</h3><br />
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</div><br />
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<div style="width: 97%; float: left;"></div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week&diff=533032010 Summer Project Week2010-06-03T20:15:57Z<p>Arnaudgelas: /* 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 Ibanesz)<br />
**3-4pm: 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, Fill in Dates]]<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/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 />
<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)<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 Meir, Hans Johnson)<br />
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)<br />
* Liver Ablation (Haiying Liu)<br />
* BrainLab-Aurora HybridNav (Isaiah Norton, Dan Marcus)<br />
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)<br />
<br />
=== Radiotherapy ===<br />
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp)<br />
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)<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 />
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)<br />
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)<br />
<br />
===[[Microscopy Image Analysis]] ===<br />
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard<br />
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more<br />
* Gouaillard: Flow Cytometry<br />
* [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)<br />
* Arnaud Gelas, Sean Megason, Badri Roysam: Wrapping FARSIGHT nuclear segmentation algorithm as a GoFigure plugin.<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 />
* Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason, Badri Roysam: Seeding results comparison<br />
* [[ITK GPAC level set]] (K. Palaniappan, Kishore Mosaliganti, Sean Megason)<br />
<br />
=== Shape Analysis ===<br />
* Median Shape by Boundary-based Distance (Tammy Riklin Raviv, Sylvain Bouix)<br />
=== Informatics ===<br />
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)<br />
<br />
=== Diffusion ===<br />
*Fluid Mechanics Based Tractography (Nathan Hageman)<br />
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)<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 />
*XNAT Enterprise webservices client for Slicer (Wendy, Mark)<br />
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)<br />
<br />
*VTKWidgets (JC, will, Schroeder, Nicole, Ron)<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 />
#Aucoin, Nicole, BWH<br />
#Audette, Michel, Kitware<br />
#Aylward, Stephen, Kitware, Inc<br />
#Boucharin, Alexis, UNC Neuro Image Research and Analysis Laboratories<br />
#Bouix, Sylvain, BWH<br />
#Budin, Francois, UNC<br />
#Burdette, Everette, Acoustic MedSystems, Inc.<br />
#Chen, Min, Johns Hopkins University<br />
#Datar, Manasi, SCI Institute<br />
#Eckbo, Ryan, BWH<br />
#Fedorov, Andriy, Surgical Planning Lab<br />
#Fillion-Robin, Jean-Christophe, Kitware Inc.<br />
#Finet, Julien, Kitware Inc<br />
#Fishbaugh, James, SCI Institute<br />
#Gao, Yi, Gerogia Tech<br />
#GELAS, Arnaud, Harvard Medical School<br />
#gouaillard, alexandre, CoSMo Software<br />
#Gouttard, Sylvain, SCI Institute<br />
#Haehn, Daniel, University of Pennsylvania<br />
#Hageman, Nathan <br />
#Hahn, Dieter, University Erlangen<br />
#Hamel, Corentin, UNC Chapel Hill<br />
#Hata, Nobuhiko, Brigham and Women's Hospital<br />
#Hayes, Kathryn, Brigham and Women's Hospital<br />
#Holton, Leslie, Medtronic Navigation<br />
#Ibanez, Luis, KITWARE Inc.<br />
#Johnson, Hans, University of Iowa<br />
#Kapur, Tina, Brigham and Women's Hospital<br />
#Kikinis, Ron, Brigham and Women's Hospital<br />
#Kim, Minjeong, UNC-Chapel Hill<br />
#Kolesov, Ivan, Georgia Institute of Technology<br />
#Larson, Garrett, UNC-CH<br />
#Li, Rui, MGH<br />
#Lisle, Curtis, KnowledgeVis, LLC<br />
#Liu, Haiying, Brigham and Women's Hospital<br />
#Liu, Yanling, SAIC-Frederick, Inc.<br />
#Magnotta, Vincent, The University of Iowa<br />
#malaterre, mathieu, CoSMo Software<br />
#Mastrogiacomo, Katie, Brigham and Women's Hospital<br />
#Matsui, Joy, University<br />
#Megason, Sean, Harvard Medical School<br />
#Meier, Dominik, BWH, Boston MA<br />
#menze, bjoern, CSAIL MIT<br />
#Mosaliganti, Kishore, Harvard Medical School<br />
#Niethammer, Marc, UNC Chapel Hill<br />
#Norton, Isaiah, BWH Neurosurgery<br />
#Paniagua, Beatriz, University of North Caolina at Chapel Hill<br />
#Papademetris, Xenophon, Yale University<br />
#Partyka, David, Kitware Inc<br />
#Pathak, Sudhir, Univeristy Of Pittsburgh<br />
#Peroni, Marta, Politecnico di Milano<br />
#Perrot-Audet, Antonin, Harvard Medical School<br />
#Pieper, Steve, Isomics, Inc.<br />
#Plesniak, Wendy, BWH<br />
#Pohl, Kilian, IBM<br />
#Pujol, Sonia, Brigham and Women's Hospital<br />
#Rannou, Nicolas, Harvard Medical School<br />
#Riklin Raviv, Tammy, MIT, CSAIL<br />
#Ruiz, Marco, UCSD<br />
#Schroeder, William, Kitware<br />
#Scully, Mark, The Mind Research Network<br />
#Sharp, Greg, MGH<br />
#Shi, Yundi, UNC Chapel Hill<br />
#Shusharina, Nadya, MGH<br />
#Smith, Gareth, Wolfson Medical Imaging Centre (WMIC)<br />
#Souhait, Lydie, Harvard Medical School<br />
#Spinczyk, Dominik, Silesian University of Technology<br />
#Srinivasan, Padmapriya <br />
#Tao, Xiaodong, GE Research<br />
#Ungi, Tamas, Queen's University<br />
#Vachet, Clement, UNC Chapel Hill<br />
#Veni, Gopalkrishna, SCI Institute<br />
#Wassermann, Demian, SPL/LMI/PNL<br />
#Wells, Sandy, BWH<br />
#Wu, Guorong, University of North Carolina at Chapel Hill</div>Arnaudgelashttps://www.na-mic.org/w/index.php?title=ITK_GPAC_level_set&diff=53302ITK GPAC level set2010-06-03T20:13:10Z<p>Arnaudgelas: Created page with '==Key Investigators== * University of Missouri: K. Palaniappan * Harvard Medical School: Kishore Mosaliganti <div style="margin: 20px;"> <div style="width: 27%; float: left; pad…'</p>
<hr />
<div>==Key Investigators==<br />
* University of Missouri: K. Palaniappan<br />
* Harvard Medical School: Kishore Mosaliganti<br />
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<div style="margin: 20px;"><br />
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<h3>Objective</h3><br />
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<h3>Approach, Plan</h3><br />
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<div style="width: 40%; float: left;"><br />
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<h3>Progress</h3><br />
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<div style="width: 97%; float: left;"></div>Arnaudgelas