2016 Summer Project Week

2016-06-25T09:00:59Z

MarcoNolden: fixed link

__NOTOC__

[[image:PW-Summer2016.png|300px]]
<br><br>

<font color="maroon" size="5">Please fill in the survey about project weeks today!</font>

<font size="5">
[https://hms.az1.qualtrics.com/jfe/form/SV_6gK6BFe4Ivfo9RH click here]
</font>

<br><br>

<font color="maroon" size="5">Please hold January 9-13, 2017 for Project Week#24 at MIT. </font>

<br><br>

<font color="maroon" size="5">Please hold June 16-24 for Project Week#25 in Europe. It will be either right before IPCAI (i.e June ~16-20) or right after CARS! (~June 25-29)</font>

<br><br>

<br><br>

<font color="maroon" size="5"> Please add photos from this week here: https://goo.gl/photos/Dhx6Fdei27NZe2rX9

<br><br>

</font>

=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week open source hackathon is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS) and the [http://www.ipcai.org/ IPCAI 2016] conferences in Heidelberg, Germany. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

='''Agenda'''=
<font color="maroon">Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS</font>
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:7%" |Time
!style="width:15%" |Monday, June 20 <br> [https://goo.gl/maps/e3ZbcsM5KC82 DKFZ]
!style="width:3%" |Tuesday, June 21 <br> IPCAI
!style="width:15%" |Wednesday, June 22 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Thursday, June 23 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Friday, June 24 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Saturday, June 25 <br> Congress Hall of CARS, Room Trübnersaal
|-
|bgcolor="#ffffdd"|'''9:00am-10:00am'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="8"|
|bgcolor="#ffffff"|[[{{FULLPAGENAME}}/Workshop_on_Shared_Software_Platform_for_Ultrasound-Guided_Medical_Interventions|Workshop: Ultrasound-guided interventions software platform (all day)]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''10:00am-10:30am'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''10:30-12pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| 10:30am-12pm: Progress Review
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch and adjourn
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"| Welcome! <br> Project Introductions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="4"|
|-
|bgcolor="#ffffdd"|'''3:00pm-3:30pm'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''3:30pm-5:00pm'''
|bgcolor="#ffffff"| What does a Neurosurgeon need from technologists? (Alexandra Golby, MD)
|bgcolor="#ffffff"| [[{{FULLPAGENAME}}/Breakout Session Slicer Extensions|Breakout Session: Slicer Extensions]] (JC, Steve)
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|}

='''Projects'''=

* Note: Please use this [[2016_Summer_Project_Week_Template | template]] to create project pages

=== Worldwide Ultrasound Navigation ===
Over the last several PWs, an international group has emerged for collaborative specification and development of ultrasound-based navigation for surgical and interventional radiology applications. This group represents the leadership of ultrasound navigation technology from Queens University (PERK Lab, PLUS: Andras Lasso, Tamas Ungi, Csaba Pinter, Gabor Fichtinter), Montreal Neurologic Institute (Simon Drouin), Brigham and Women's Hospital/HMS (William Wells, Steve Pieper, Sarah Frisken), Robarts Research Institute, Western University (Terry Peters, Adam Rankin), Trondheim University and SINTEF (CustusX: Christian Askeland, Frank Lindseth).

* [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Thomas Kirchner, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland)
* [[2016 Summer Project Week/Guided Ultrasound Calibration | Guided Ultrasound Calibration]] (Elvis Chen, Inês Prata, Tamas Ungi)
* [[2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink | Integrating PLUS in Applications using OpenIGTLink]] (Christian Askeland, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland, Longquan Chen, Simon Drouin)

=== Simplified Human-Computer Interactions for Intra-Operative Usage===
This theme focuses on infrastructure for simplified human-computer interactions for intra-operative usage. This includes Guidelets, simplified graphical user interfaces that can access the same backend as 3D Slicer; as well as interfaces for virtual reality/augmented reality devices from the consumer market that are that are improving by leaps and bounds and show promise for surgical use.

* [[2016 Summer Project Week/Guidelets | Guidelets (Slicelets for IGT)]] (Tamas Ungi, Andras Lasso, Thomas Vaughan)
* [[2016 Summer Project Week/Slicelet For Ultrasound Acquisition | Slicelet for Ultrasound Acquisition]] (Sarah Frisken, Prashin Unadkat, Steve Pieper, Anna Roethe)
* [[2016 Summer Project Week/OpenVR_integration | OpenVR Integration]] (Adam Rankin, Andras Lasso)
* [[2016 Summer Project Week/VRPN Integration | VRPN Integration]] (Dženan Zukić)
* [[2016 Summer Project Week/AR with a tablet device in the surgical room | AR with a Tablet Device in the Surgical Room]] (David García, Javier Pascau)
* [[2016 Summer Project Week/Auditory Display | Auditory Display Integration]] (David Black, Sarah Frisken, Christian Hansen, Longquan Chen)

===Machine Learning for IGT===
This theme applies concepts from machine learning to image-guided therapy, including the application of convolutional neural networks for segmentation of mechanically implanted devices during surgery, and the use of Gaussian processes for estimation of uncertainty in image-fusion.

* [[2016 Summer Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Guillaume Pernelle, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea, Tina Kapur)
* [[2016 Summer Project Week/Uncertainty-aware Information Fusion | Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation]] (Bojan Kocev, Sarah Frisken, Christian Hansen, William Wells)

===IGT Other===
* [[2016 Summer Project Week/SliceTracker | SliceTracker for Data Collection and Prostate Biopsy Support ]] (Christian Herz, Peter Behringer, Andrey Fedorov)
* [[2016 Summer Project Week/Intra-procedural prostate motion characterization | Prostate Motion Characterization ]] (Peter Behringer, Christian Herz, Andrey Fedorov)
* [[2016 Summer Project Week/Structural-functional measurements | Structural - Functional Relationship Measurements of Tractography Data with fMRI ]] (Yannick Suter, Lauren J. O'Donnell)
* [[2016 Summer Project Week/Sacral Neuromodulation | Sacral Neuromodulation ]] (Rocío López, Javier Pascau, Tamas Ungi)
* [[2016 Summer Project Week/Histological Brain Atlas | Tool for the construction of an integrated brain atlas based on histology and MRI to aid Deep Brain Stimulation]] (Fernando Pérez García)
* [[2016 Summer Project Week/Integrating/Using OpenIGTLink for the communications of Robotics devices | Integrating/Using OpenIGTLink for the Communications of Robotics Devices]] (Scheherazade Kraß, Longquan Chen)
* [[2016 Summer Project Week/Intraoperative Functional Guidance workflows in Neurosurgery | Intraoperative Functional Guidance Workflows in Neurosurgery]] (Prashin Unadkat, Sarah Frisken, Anna Roethe, Christian Hansen)

=== Informatics ===
This theme deals with creating data formats to enable medical image informatics. Led by the [http://qiicr.org/about.html QIICR project], the results will be made available in the DICOM for Quantitative Imaging (DCMQI) Library for sharing quantitative image-processing results in a standardized way.

* [[2016 Summer Project Week/dcmqi | DICOM for Quantitative Imaging (dcmqi) Library]] (Andrey Fedorov, Christian Herz, Marco Nolden, Hans Meine, Csaba Pinter, Steve Pieper, et al)
* [[2016 Summer Project Week/DICOM Parametric Maps | Finalizing DICOM Parametric Map Implementation in DCMTK for QIICR project]] (Michael Onken, Jan Schlamelcher, Andrey Fedorov, Christian Herz)
* [[2016 Summer Project Week/MeVisLab SEG Colors | Support Reading and Writing DICOM Tags for SEG Colors]] (Hans Meine, Andrey Fedorov)
* [[2016 Summer Project Week/Segmentation Editor and Terminology | Segmentation Editor and Terminology]] (Nicole Aucoin, Andrey Fedorov, Csaba Pinter, Andras Lasso, Marco Nolden, Christian Herz)

=== Infrastructure ===
Improvements to the core functionality of widely used open source tools is an on-going theme.

* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)
* [[2016 Summer Project Week/3D Lasso Selection | Implementation and Testing Performance of 3-D Lasso Selection within the Segmentation Editor Infrastructure ]] (Davide Punzo, Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2016 Summer Project Week/Segmentations Integration | Integration of Segmentations Infrastructure and Related Modules to Slicer Core]] (Csaba Pinter, Andras Lasso)
* [[2016 Summer Project Week/DICOM Tractography Results | Finalizing DICOM Tractography Results Implementation in DCMTK for BWH Project]] (Lauren O'Donnell, Isaiah Norton, Michael Onken)
* [[2016 Summer Project Week/Curve and Surface Creation from Fiducials|Curve and Surface Creation from Fiducials]] (Thomas Vaughan, Junichi Tokuda)
* [[2016 Summer Project WEB and 3D DICOM viewer to the rest of us]] (Koji Kobayashi, Steve Pieper)
* [[2016 Summer Project Week/CommonGL|CommonGL: GPU Rendering and Computation]] (Steve Pieper, Christian Askeland, Andra Lasso, Simon Drouin, Fernando Pérez García)

=== Tutorial===
Creation of tutorials and documentation is an on-going theme.

* [[2016 Summer Project Week/SlicerDMRIDocumentation | Tutorials and Documentations in SlicerDMRI]] (Lauren J. O'Donnell, Fan Zhang, Isaiah Norton)
* [[2016 Summer Project Week/UniversityCourse | Create the basics of a university course about medical image computing]] (Attila Nagy)
* [[2016 Summer Project Week/CameraTutorial | How to use Basler Cameras for Medical Applications]] (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)

='''Logistics'''=
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
==Location==
*'''Location:''' Heidelberg, Germany.
**'''Getting to Heidelberg:''' Most will fly into Frankfurt Main International (FRA). At the airport look for "long distance trains". There you can buy a ticket from the machine to Heidelberg Hauptbahnhof (main station), around EUR 25. It usually takes less than an hour, with a change in Mannheim to a regional train. https://www.bahn.de . If you arrive on Sunday you can take a bus from the station to the Old Town or where your hotel is. Heidelberg is pretty small, look for directions on Google Maps. If you arrive on Monday see below on how to get to DKFZ directly.
**'''Monday''' at German Cancer Research Center - DKFZ
*** Enter through the main lobby ( just north of https://goo.gl/maps/e3ZbcsM5KC82, you can't miss it, it's the tallest building on campus with a big "dkfz." on top). The meeting room is on the 8th floor (H824, "Glaskasten", "glass box"). We will leave some instructions how to get there at the reception. The meeting time in the lobby will be 8:45am for those who wish to be at the meeting room by 9am. Official activities will start at noon with lunch.
*** To get to DKFZ in the morning you can use the Google Maps link above, public transport information is available there. For people staying in the Old Town, near Bismarckplatz or coming from the station it will be most likely Bus #32, exit at stop "Chirurgische Klinik", which is the second one after crossing the Neckar river. More detailed timetables at [http://fahrplanauskunft.vrn.de/vrn/XSLT_TRIP_REQUEST2?language=en the local transportation services VRN]. If you are up early there is also a nice [https://goo.gl/maps/SRRG6x7KDNU2 walk along the river].
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
***Suggested place for meetings is the Marstall student center ([https://www.google.de/maps/place/Zeughaus-Mensa+im+Marstall/@49.4124525,8.7056926,349m/data=!3m1!1e3!4m5!3m4!1s0x0000000000000000:0x8fd41be2e27fc36e!8m2!3d49.412919!4d8.7044381 map])
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
==Preparatory Conference Calls: ==
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.
**Call #3 Tuesday, May 31, 9am Boston time.
**Call #4 Tuesday, Jun 7, 9am Boston time.
**Call #5 Tuesday, Jun 14, 9am Boston time.

=='''Equipment'''==
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)
*[[2016_Summer_Project_Week:Equipment_Requests|Specialized equipment that people would like to have]] '''Updated June 16 2016'''

= '''Registrants''' =

'''REGISTRATION:''' Please add your name to this list if you are definitely planning to attend. If you are not already on it, please add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]. We need to know the number of people at DKFZ, so if you are there on Monday, please add "(Mon)" next to your name. Official registration for the event is through the CARS conference at http://www.cars-int.org/cars_2016/registration.html -- which you can do now or onsite.

# Tina Kapur, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA (Mon)
# Ron Kikinis, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA and University of Bremen / Fraunhofer MEVIS, Germany (Mon)
# Dženan Zukić, Kitware, USA
# Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal. (Mon)
# Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School (Mon)
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Steve Pieper, Isomics, Inc., USA (Mon)
# Nicole Aucoin, Brigham and Women's Hospital (Mon)
# Simon Drouin, Montreal Neurological Institute (Mon)
# Thomas Kirchner, German Cancer Research Center (Mon)
# Elvis Chen, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Adam Rankin, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Christian Askeland, SINTEF, Norway (Mon)
# Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany (Mon)
# Longquan Chen, BWH/HMS, Boston, USA (Mon)
# Davide Punzo, Kapteyn Astronomical Institute, Netherlands (Mon)
# Lauren O'Donnell, BWH/HMS (Mon)
# Yannick Suter, BWH/HMS (Mon)
# Junichi Tokuda, BWH/HMS (Mon)
# Sarah Frisken, BWH/HMS (Mon)
# Prashin Unadkat, BWH/HMS
# Anna Roethe, Charite, Berlin
# Michael Onken, Open Connections, Germany (Mon)
#Jan Schlamelcher, Open Connections/OFFIS, Germany
# Janne Beate Bakeng, SINTEF, Norway
# Ole Vegard Solberg, SINTEF, Norway
# Jon Eiesland, SINTEF, Norway
# Tamas Ungi, Queen's University, Canada (Mon)
# Andras Lasso, Queen's University, Canada (Mon)
# Csaba Pinter, Queen's University, Canada (Mon)
# Thomas Vaughan, Queen's University, Canada (Mon)
# Javier Pascau, Universidad Carlos III de Madrid, Spain (Mon)
# Verónica García-Vazquez, Universidad Carlos III de Madrid, Spain (Mon)
# Mónica García-Sevilla, Universidad Carlos III de Madrid, Spain (Mon)
# David García-Mato, Universidad Carlos III de Madrid, Spain (Mon)
# Rocío López-Velazco, Universidad Carlos III de Madrid, Spain (Mon)
# Raúl San José, BWH/HMS, Boston
# Pietro Nardeli, BWH/HMS, Boston
# Andrey Fedorov, BWH/HMS, Boston (Mon, Wed, Thu)
# Christian Herz, BWH/HMS, Boston (Mon)
# Frank Lindseth, NTNU/SINTEF, Norway
# Peter Behringer, Basler AG, Germany
# Santhirarajah Mathimugan, Basler AG, Germany
# Koji Kobayashi, Vocsis Corporation, Japan
# David Black, University of Bremen / Fraunhofer MEVIS, Germany (Mon)
#William Wells, BWH/HMS (Mon)
# Attila Nagy, University of Szeged, Hungary (Mon)
# Bojan Kocev, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Sara Fernández Vidal, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Fernando Pérez García, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Marco Nolden, [http://mbi.dkfz-heidelberg.de Medical and Biological Informatics, German Cancer Research Center] (Mon)
# Christian Hansen, [http://isgwww.cs.uni-magdeburg.de/cas/ University of Magdeburg], Germany (Mon)
# Julian Hettig, [http://isgwww.cs.uni-magdeburg.de/cas/ University of Magdeburg], Germany (Mon)
# Jorge Onieva, BWH/HMS, Boston
# Caspar Goch, German Cancer Research Center (Mon)

'''Please don't forget to add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].'''

2016 Summer Project Week/Intraoperative Functional Guidance workflows in Neurosurgery

2016-06-25T08:56:46Z

MarcoNolden: MarcoNolden moved page 2016 Summer Project Week/Intraoperative Imaging workflow in Hybrid ORs to 2016 Summer Project Week/Intraoperative Functional Guidance workflows in Neurosurgery: On request ;)

==Key Investigators==
* Prashin Unadkat, BWH/HMS
* Sarah Frisken, BWH/HMS
* Anna Roethe, Charite/Humboldt University
* Christian Hansen, Otto-von-Guericke University Magdeburg

==Project Description==

Document, understand, refine and evaluate technology assisted workflows for various neurosurgical procedures in AMIGO compared to standard ORs and other hybrid ORs

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Document and refine workflows for various procedures in AMIGO.
* Also, define meaningful indications for image-guided surgical treatment in AMIGO as opposed to standard ORs
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* 5 year evaluation of Patient cases operated in AMIGO
* Analyzed and summarized current workflow patterns in AMIGO
* Reviewed the literature regarding current practices of Intra-operative Imaging
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* To be discussed at Project Week
</div>
</div>

2016 Summer Project Week/Intraoperative Imaging workflow in Hybrid ORs

2016-06-25T08:56:46Z

#REDIRECT [[2016 Summer Project Week/Intraoperative Functional Guidance workflows in Neurosurgery]]

2016 Summer Project Week/medical imaging webapp

2016-06-25T08:52:06Z

MarcoNolden:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Steve Pieper (Isomics)
* Hans Meine (Uni Bremen, MEVIS)
* Marco Nolden (DKFZ)
(other interested parties are welcome!)

==Project Description==

[[File:Ctk-web.jpg]]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Review the state of the art in medical imaging web apps
** Follow on from the [http://qiicr.org/web/outreach/MIWS-hackfest/ MIWS Hackfest at BWH].
** Discuss subsequent developments and ideas
* Consider various use cases:
** Pure web browser application
** Web browser + remote compute or rendering services
** Web App widgets used in desktop application (e.g. via QtWebKit/QtWebEngine in Slicer/MITK/MeVis)
* Topics
** Native JavaScript code for DICOM IO, Rendering, Processing
** Organization of toolkits and libraries
** Interacting with the community of like-minded developers
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discuss recent developments cited in the Objective section
* Identify more valuable development priorities
** provide useful functionality (e.g. improved DICOM patient/study/series/search browser)
** probe any outstanding issues (e.g. test scalability or performance questions)
** establish paradigms for ongoing development
* Finalize a prototype showing JS-C++ interaction replacing the CTK DICOM Browser Widget with a web-technology based implementation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Investigate emerging file distribution tools
** infinit
** ipfs
*** ipfs ls [https://ipfs.io/ipfs/QmYDwWrSPnYeE1z1Ae3me9XzT394YKy4ux5e85V4oCDakT QmYDwWrSPnYeE1z1Ae3me9XzT394YKy4ux5e85V4oCDakT]
*** Brainlab demo objects [https://ipfs.io/ipfs/QmTftaDyQCNFsceFwR2kkRMdz5VBbCzzD64VVEWiKRA2Go QmTftaDyQCNFsceFwR2kkRMdz5VBbCzzD64VVEWiKRA2Go]
* Experimental integration of ipfs-hosted data with CTest based continuous integration (WIP) https://github.com/QIICR/dcmqi/pull/22
* Identified [http://www.zerorpc.io zerorpc] as a powerful solution for distributed MIC apps (based on [http://zeromq.org ØMQ] and [http://msgpack.org MessagePack]).
** Use [https://pypi.python.org/pypi/msgpack-numpy msgpack-numpy] to support ndarrays in zerorpc (implemented via monkey-patching).
* The JS-C++ interaction lives now on an [https://github.com/nolden/CTK/tree/wip-dicom-web experimental branch in CTK] (will move to the commontk organization soon)
** various mechanisms for development, debug and deployment can be tested,
*** Qt resource compiler
*** separate HTML files
*** running the UI in a browser vs integrated in the CTK application, remote debugging of javascript (all accessible through buttons in the UI)
</div>
</div>

2016 Summer Project Week/medical imaging webapp

2016-06-25T08:41:00Z

MarcoNolden: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Steve Pieper (Isomics)
* Hans Meine (Uni Bremen, MEVIS)
* Marco Nolden (DKFZ)
(other interested parties are welcome!)

==Project Description==

[[File:Ctk-web.jpg]]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Review the state of the art in medical imaging web apps
** Follow on from the [http://qiicr.org/web/outreach/MIWS-hackfest/ MIWS Hackfest at BWH].
** Discuss subsequent developments and ideas
* Consider various use cases:
** Pure web browser application
** Web browser + remote compute or rendering services
** Web App widgets used in desktop application (e.g. via QtWebKit/QtWebEngine in Slicer/MITK/MeVis)
* Topics
** Native JavaScript code for DICOM IO, Rendering, Processing
** Organization of toolkits and libraries
** Interacting with the community of like-minded developers
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discuss recent developments cited in the Objective section
* Identify more valuable development priorities
** provide useful functionality (e.g. improved DICOM patient/study/series/search browser)
** probe any outstanding issues (e.g. test scalability or performance questions)
** establish paradigms for ongoing development
* Finalize a prototype showing JS-C++ interaction replacing the CTK DICOM Browser Widget with a web-technology based implementation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Investigate emerging file distribution tools
** infinit
** ipfs
*** ipfs ls [https://ipfs.io/ipfs/QmYDwWrSPnYeE1z1Ae3me9XzT394YKy4ux5e85V4oCDakT QmYDwWrSPnYeE1z1Ae3me9XzT394YKy4ux5e85V4oCDakT]
*** Brainlab demo objects [https://ipfs.io/ipfs/QmTftaDyQCNFsceFwR2kkRMdz5VBbCzzD64VVEWiKRA2Go QmTftaDyQCNFsceFwR2kkRMdz5VBbCzzD64VVEWiKRA2Go]
* Experimental integration of ipfs-hosted data with CTest based continuous integration (WIP) https://github.com/QIICR/dcmqi/pull/22
* Identified [http://www.zerorpc.io zerorpc] as a powerful solution for distributed MIC apps (based on [http://zeromq.org ØMQ] and [http://msgpack.org MessagePack]).
** Use [https://pypi.python.org/pypi/msgpack-numpy msgpack-numpy] to support ndarrays in zerorpc (implemented via monkey-patching).
* The JS-C++ interaction lives now on an experimental branch in commontk/CTK
** various mechanisms for development, debug and deployment can be tested,
*** Qt resource compiler
*** separate HTML files
*** running the UI in a browser vs integrated in the CTK application, remote debugging of javascript (all accessible through buttons in the UI)
</div>
</div>

2016 Summer Project Week/medical imaging webapp

2016-06-20T11:13:12Z

MarcoNolden:

2009-06-30T14:08:14Z

MarcoNolden: /* What are the goals of a common toolkit? */ protocol of day2

__NOTOC__
=The Common Toolkit Workshop at the [http://www.dkfz.de/index.html DKFZ] in Heidelberg, Germany hosted by the [http://www.dkfz-heidelberg.de/en/mbi/index.html MBI].=

{|
|align="left"|The purpose of this workshop was to convene a number of groups who are working on FOSS Medical Image Computing platform development using '''BSD''' style licenses and to explore meaningful ways of coordination and integration. Day one of the meeting consisted of briefing each other about the softwares, day two was for brainstorming and concept development.
|[[image:Heidelberg corr.jpg|thumb|250px|<big>Heidelberg</big><br>Source: http://upload.wikimedia.org/wikipedia/commons/b/b4/Heidelberg_corr.jpg]]
|}

=Day 1=
June 29 2009
Presentation of platform / toolkit efforts. Names of the actual presenters are listed.

<gallery widths="150px" heights="150px" perrow="4">
image:KitwareLogo2.jpg|[[media:CTK-KitwareOverview-Aylward.ppt|ITK, VTK, IGSTK, InfoVis, FARSIGHT, Maverick]] (Stephen Aylward)
image:3DSlicerLogo-H-Color-424x236.png|[[media:3D-Slicer-presentation-June-29-2009.ppt|Slicer3]] (Ron Kikinis, Steve Pieper)
image:INRIAlogo.png|[[media:MedINRIA-presentation-June-29-2009.ppt|MedINRIA]] (Olivier Clatz, Julien Wintz)
image:Siemens-logo.jpg|[[media:SCR_CTK_XIP.pdf|OpenXIP Extensible Imaging Platform]] (Gianluca Paladini)
image:B3C.png|[[media:Pres_maf3_Heidelberg2009.pdf‎|MAF3]] (Paolo Quadrani)
image:Mitk-logo.png|[[media:MITK-CTK-Workshop-June2009.ppt‎|MITK]] (Ivo Wolf, Marco Nolden)
image:WashU logo.jpg|Working Group 23 (Lawrence Tarbox)
image:RadPharmLogo.gif|[[media:CTK_2009_Heidelberg_Clunie.ppt|What can we learn from PACS development]] (David Clunie)
</gallery>

=Day 2=
==What are the goals of a common toolkit?==

===First ideas from day 1===

* Very modular architecture
* Common core:
** e.g. IO of scenes
** common object layer (?)
** should be GUI independent
* Not be trying to address everything …
** … within the CTK core
** leave different tasks to different toolkits/applications on top of CTK
** OR: … optional parts of CTK (on top of the CTK core)
* Extensible, scriptable end-user application(s) (also optional; host)
** different applications for clinicians, for biomedical researchers
* Offer commercial support

=== Discussion result day 2===

==== Legal and regulatory aspects ====

* License: BSD-style
* Common, transatlantic license regarding liability
* No inclusion of patents unless we are granted a license to use it

* Appropriate process and tools to ease quality management
** Coding convention
** Unit testing
** Design documentation
** Support traceability

====General====

* Common repository: not just a list of toolkits, but includes some CTK specific code (CTK core)
** Basic functionality that we all need

====Technical aspects====
* Language of core library: C++
** But language bindings to other languages: Java, Python, .NET
** Automated binding generation
* Reuse methods available in Qt by default
* IO layer
** base Qt-independent
** on top: Qt-dialogs etc.
** Support many file formats
** Allow storage of scene graphs
** Should be DICOM-centric
*** DICOM support has to be designed that it can evolve -> modular
*** taken from existing toolkits (e.g. DCMTK), but
**** consolidate at common place
**** add missing features
*** adaptors that allow to leave the actual IO to the host
*** Example: “save scene as DICOM”
* GUI-part must be separable
* C++/Qt reference implementation of WG23 host
* Include a database (but allow other databases to be used)
* Single click installation for users
* Single click installation for developers

====Scope====
* IO layer
* GUI- wizard Workflow
* scripting language support
* plugin loading mechanism

* IGT support?
* Robotics support?
* Control of devices?

==Next steps==
* Form a consortium:
** Participants of this meeting, OFFIS, Kevin Cleary
** Mailing list
* Grants
** Inform each other of grant applications
** Mention CTK in the grant applications
* Webpage on www.CommonTK.org incl. logo
* Next meeting: Sept 25th (full day)

==Follow up meeting==
1 full day meeting in Oxford, UK after MICCAI, Friday, September 25 2009

==Funding opportunities==
===Europe===

===USA===
* [[Collaborator:FAQ_for_funding_via_NIH_PAR-06-223|NA-MIC collaboration PAR]]
* [http://grants.nih.gov/grants/guide/pa-files/PAR-08-010.html Software maintenance grants]

Events:CTK-Workshop-June-2009

2009-06-30T09:18:33Z

MarcoNolden: /* Day 1 */ Changed MITK logo

=The Common Toolkit Workshop at the [http://www.dkfz.de/index.html DKFZ] in Heidelberg, Germany hosted by the [http://www.dkfz-heidelberg.de/en/mbi/index.html MBI].=

The purpose of this workshop was to convene a number of groups who are working on FOSS Medical Image Computing platform development using BSD style licenses and to explore meaningful ways of coordination and integration. Day one of the meeting consisted of briefing each other about the softwares, day two was for brainstorming and concept development.

=Day 1=
June 29 2009
Presentation of platform / toolkit efforts. Names of the actual presenters are listed.
<gallery widths="150px" heights="150px" perrow="4">
image:KitwareLogo2.jpg|[[media:CTK-KitwareOverview-Aylward.ppt|ITK, VTK, IGSTK, InfoVis, FARSIGHT, Maverick]] (Stephen Aylward)
image:3DSlicerLogo-H-Color-424x236.png|[[media:3D-Slicer-presentation-June-29-2009.ppt|Slicer3]] (Ron Kikinis, Steve Pieper)
image:INRIAlogo.png|[[media:MedINRIA-presentation-June-29-2009.ppt|MedINRIA]] (Olivier Clatz, Julien Wintz)
image:Siemens-logo.jpg|[[media:SCR_CTK_XIP.pdf|OpenXIP Extensible Imaging Platform]] (Gianluca Paladini)
image:B3C.png|[[media:Pres_maf3_Heidelberg2009.pdf‎|MAF3]] (Paolo Quadrani)
image:Mitk-logo.png|[[media:MITK-CTK-Workshop-June2009.ppt‎|MITK]] (Ivo Wolf, Marco Nolden)
image:3DSlicerLogo-H-Color-424x236.png|Working Group 23 (Lawrence Tarbox)
image:3DSlicerLogo-H-Color-424x236.png|What can we learn from PACS development (David Clunie)
</gallery>

=Day 2=

File:Mitk-logo.png

2009-06-30T09:15:40Z

MarcoNolden: