NAMIC Wiki - User contributions [en]

2017 Winter Project Week/OAuth2SlicerPathology

2016-12-14T15:33:56Z

Ebremer:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* [http://ebremer.com Erich Bremer] ([https://bmi.stonybrookmedicine.edu Stony Brook Medicine])

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Enable [https://oauth.net/2/ OAuth 2.0] authentication within [https://github.com/SBU-BMI/SlicerPathology SlicerPathology] for purposes of authenticating with various web resources.

|

* Direct [https://oauth.net/2/ OAuth 2.0] authentication using python
** Identify any needed support libraries that are compatible with 3D Slicer license.
* Also checking to extend SlicerPathology's use of WebKit to achieve OAuth 2.0 authentication.
|

*
|}

==Background and References==

2017 Winter Project Week/OAuth2SlicerPathology

2016-12-14T15:33:12Z

Ebremer:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* [http://ebremer.com Erich Bremer] ([https://bmi.stonybrookmedicine.edu Stony Brook Medicine])

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Enable [https://oauth.net/2/ OAuth 2.0] authentication within [https://github.com/SBU-BMI/SlicerPathology SlicerPathology] for purposes of authenticating with various web resources.

|

* Direct [https://oauth.net/2/ OAuth 2.0] authentication using python
** Identify any needed support libraries that are compatible with 3D Slicer license.
* Also checking extending SlicerPathology's use of WebKit to achieve OAuth 2.0 authentication
|

*
|}

==Background and References==

2017 Winter Project Week/OAuth2SlicerPathology

2016-12-14T15:32:29Z

Ebremer:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* [http://ebremer.com Erich Bremer] ([https://bmi.stonybrookmedicine.edu Stony Brook Medicine])

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Enable OAuth 2.0 authentication within [https://github.com/SBU-BMI/SlicerPathology SlicerPathology] for purposes of authenticating with various web resources.

|

* Direct [https://oauth.net/2 OAuth2.0] authentication using python
** Identify any needed support libraries that are compatible with 3D Slicer license.
* Also checking extending SlicerPathology's use of WebKit to achieve OAuth 2.0 authentication
|

*
|}

==Background and References==

2017 Winter Project Week/OAuth2SlicerPathology

2016-12-14T15:31:52Z

Ebremer:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* [http://ebremer.com Erich Bremer] ([https://bmi.stonybrookmedicine.edu Stony Brook Medicine])

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Enable OAuth 2.0 authentication within [https://github.com/SBU-BMI/SlicerPathology SlicerPathology] for purposes of authenticating with various web resources.

|

* Direct [https://oauth.net/2/ OAuth 2.0] authentication using python
** Identify any needed support libraries that are compatible with 3D Slicer license.
* Also checking extending SlicerPathology's use of WebKit to achieve OAuth 2.0 authentication
|

*
|}

==Background and References==

2017 Winter Project Week

2016-12-14T15:30:20Z

Ebremer: Added OAuth 2.0 in SlicerPathology

__NOTOC__
[[image:PW-Winter2017.png|300px]]

=Welcome to the web page for the 24th Project Week!=

The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. 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].

==Logistics==

*'''Dates:''' January 9-13, 2017.
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.

== Introduction ==
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], enhancements to the underlying building blocks [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an open source hackathon event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 researchers. As of August 2014, it is a [http://www.miccai.org/organization MICCAI] endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO].

A summary of all previous Project Events is available [[Project_Events#Past_Project_Weeks|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list]

==Conference Calls for Preparation==

Conference call phone number and notes are available [[TCONS:2007_Winter_Project_Week|here]].

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 9
!style="width:18%" |Tuesday, January 10
!style="width:18%" |Wednesday, January 11
!style="width:18%" |Thursday, January 12
!style="width:18%" |Friday, January 13
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#faedb6"| '''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|rowspan="2"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-10:30am'''
|bgcolor="#88aaae"|Prostate Clinical Discussion with Clare Tempany (to be confirmed)
|bgcolor="#88aaae"|9:00am-10:00am: Shape Analysis Breakout ---- ---- ---- ---- ---- ---- 10:00am-12:00pm: Luis Ibanez TensorFlow Workshop (to be confirmed)
|bgcolor="#88aaae"|Prostate Cancer: Quantitative Imaging Network Discussion with Fiona Fennessy
|bgcolor="#88aaae"|Clinical Topics
|-
|bgcolor="#ffffdd"|'''10:30am-12pm:'''
|'''Talk (Sebastian Ourselin, PhD, UCL)'''
|
|
|
|Project Reporting
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1:00-5:30pm'''
|'''1:00pm-2:30pm:''' Project Presentations
|
|
|
|'''1:30-2:30pm:''' [[AMIGO_TourPW2017Winter|AMIGO Tour]]
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day [[2017_Winter_Project_Week/Dinner|Dinner on Thursday Night]] (Optional)
|
|}

==Calendar==

'''''The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.''''' 

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20170108/20170114
}}

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

='''Projects'''=

*Use this [[2017_Project_Week_Template | Updated Template for project pages]]

== Learning and GPUs ==

== Web Technologies ==
* [[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer)

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin)

== IGT ==
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)
* [[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)

== Craniofacial ==

== Infrastructure ==
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)
* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)

== DICOM ==

==To be Categorized==

* [[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)

= '''Registrants''' =

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/2017projectweek registration site].

# Peter Anderson :: Retired
# Johan Andruejol :: Kitware, Inc.
# Janne Beate Bakeng :: SINTEF
# Andrew Beers :: Massachusetts General Hospital
# Jorge Luis Bernal Rusiel :: Boston Children's Hospital
# Laurent Chauvin :: ETS
# Alexis Girault :: Kitware, Inc.
# Polina Golland :: Massachusetts Institute of Technology
# Shun Gong :: Brigham and Women's Hospital
# Ron Kikinis :: Brigham and Women's Hospital
# Katie Mastrogiacomo :: Brigham and Women's Hospital
# Beatriz Paniagua :: Kitware, Inc.
# Chintan Parmar :: DFCI-Harvard Medical School
# Steve Pieper :: Isomics, Inc.
# Frank Preiswerk :: Brigham and Women's Hospital
# Patmaa Sridharan :: University of Pennsylvania-CBICA
# Roman Zeleznik - DFCI
# Miaomiao Zhang - Massachusetts Institute of Technology

2017 Winter Project Week/OAuth2SlicerPathology

2016-12-14T15:27:35Z

Ebremer:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* [http://ebremer.com Erich Bremer] ([https://bmi.stonybrookmedicine.edu Stony Brook Medicine])

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Enable OAuth 2.0 authentication within SlicerPathology for purposes of authenticating with various web resources.

|

* Direct OAuth 2.0 authentication using python
** Identify any needed support libraries that are compatible with 3D Slicer license.
* Also checking extending SlicerPathology's use of WebKit to achieve OAuth 2.0 authentication
|

*
|}

==Background and References==

2017 Winter Project Week/OAuth2SlicerPathology

2016-12-14T15:27:12Z

Ebremer:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* [https://ebremer.com Erich Bremer] ([https://bmi.stonybrookmedicine.edu Stony Brook Medicine])

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Enable OAuth 2.0 authentication within SlicerPathology for purposes of authenticating with various web resources.

|

* Direct OAuth 2.0 authentication using python
** Identify any needed support libraries that are compatible with 3D Slicer license.
* Also checking extending SlicerPathology's use of WebKit to achieve OAuth 2.0 authentication
|

*
|}

==Background and References==

2017 Winter Project Week/OAuth2SlicerPathology

2016-12-14T15:26:43Z

Ebremer: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* [https://ebremer.com Erich Bremer] ([https://bmi.stonybrookmedicine.edu Stony Brook Medicine])

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Enable OAuth 2.0 authentication within SlicerPathology for purposes of authenticating with various web resources.

|

* Direct OAuth 2.0 authentication using python
** Identify support libraries that are compatible with 3D Slicer license.
* Also checking extending SlicerPathology's use of WebKit to achieve OAuth 2.0 authentication
|

*
|}

==Background and References==

2017 Winter Project Week/OAuth2SlicerPathology

2016-12-14T15:25:31Z

Ebremer: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* [https://ebremer.com Erich Bremer] ([https://bmi.stonybrookmedicine.edu Stony Brook Medicine])

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Enable OAuth 2.0 authentication within SlicerPathology for purposes of authenticating with various web resources.

|

* Direct OAuth 2.0 authentication using python
** Identify support libraries that are compatible with 3D Slicer license.

|

*
|}

==Background and References==

2017 Winter Project Week/OAuth2SlicerPathology

2016-12-14T15:19:13Z

Ebremer: Created page with "__NOTOC__ <gallery> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|Projects List <!-- Use the "Upload file" link on the l..."

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2016-01-08T05:09:09Z

Ebremer: /* Project Description */

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==


* Erich Bremer - [https://bmi.stonybrookmedicine.edu/ Stony Brook University]
* Yi Gao - [https://bmi.stonybrookmedicine.edu/ Stony Brook University]
* Nicole Aucoin - [http://www.brighamandwomens.org/ Brigham and Women's Hospital]
* Andrey Fedorov - [http://www.brighamandwomens.org/ Brigham and Women's Hospital]
* Kelli Xu - [http://www.mit.edu/ MIT]

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Create intuitive and user-friendly GUI
* make meta-data exportable
* Prepare extension for Phase II cloud work and future modules
|

* create work-flow module walking user through needed steps
* wrap editor module to allow for customization for segmentation purposes without interfering with global editor instance
* capture needed data elements and export them as [http://www.w3.org/TR/json-ld/ JSON-LD] supplementing exporting of masks
* augment GUI by requesting authentication information for [http://oauth.net/2/ OAuth 2.0] and adding elements for image selection via web.
* refactor existing extension modules into separate distinct editor effects modules (currently lumped as one)
|

* initial work-flow module created
* editor module wrapped and including in one of the step tabs of the work-flow module
* label mask saved, still need to add additional meta data (algorithm parameters) as JSON-LD export
* username/password entries added to work-flow module for future web authentication
* original single editor-effect refactored into separate effects. Further cleaning of of code needed
* future work - allow image tiles to be select via web interface and resultant label masks and meta data to be exported directly to web services using OAuth2 authenication
* remove unneeded GUI elements and set additional field automatically. Create better tab icons!
* test SlicerPathology with new OpenCV Extension
|}

[[File:SlicerPathologybeginworkweek2016.png|600px|thumb|left|SlicerPathology extension at the start of Winter Work Week 2016]]
[[File:Afterworkweek.png|600px|thumb|left|SlicerPathology extension at the end of Winter Work Week 2016]]

==Background and References==


* [https://github.com/SBU-BMI/SlicerPathology SlicerPathology extension source repository]
* [http://interactivemedical.org/imic2014/CameraReadyPapers/Paper%204/IMIC_ID4_FastGrowCut.pdf Fast Growcut]

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2016-01-08T04:56:38Z

Ebremer:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==


* Erich Bremer - [https://bmi.stonybrookmedicine.edu/ Stony Brook University]
* Yi Gao - [https://bmi.stonybrookmedicine.edu/ Stony Brook University]
* Nicole Aucoin - [http://www.brighamandwomens.org/ Brigham and Women's Hospital]
* Andrey Fedorov - [http://www.brighamandwomens.org/ Brigham and Women's Hospital]
* Kelli Xu - [http://www.mit.edu/ MIT]

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Create intuitive and user-friendly GUI
* make meta-data exportable
* Prepare extension for Phase II cloud work and future modules
|

* create work-flow module walking user through needed steps
* wrap editor module to allow for customization for segmentation purposes without interfering with global editor instance
* capture needed data elements and export them as [http://www.w3.org/TR/json-ld/ JSON-LD] supplementing exporting of masks
* augment GUI by requesting authentication information for [http://oauth.net/2/ OAuth 2.0] and adding elements for image selection via web.
* refactor existing extension modules into separate distinct editor effects modules (currently lumped as one)
|

* initial work-flow module created
* editor module wrapped and including in one of the step tabs of the work-flow module
* basic meta-data captured as part of label mask save
* username/password entries added to work-flow module for future web authentication
* original single editor-effect refactored into separate effects. Further cleaning of of code needed
* future work - allow image tiles to be select via web interface and resultant label masks and meta data to be exported directly to web services using OAuth2 authenication
* remove unneeded GUI elements and set additional field automatically. Create better tab icons!
* test SlicerPathology with new OpenCV Extension
|}

[[File:SlicerPathologybeginworkweek2016.png|600px|thumb|left|SlicerPathology extension at the start of Winter Work Week 2016]]
[[File:Afterworkweek.png|600px|thumb|left|SlicerPathology extension at the end of Winter Work Week 2016]]

==Background and References==


* [https://github.com/SBU-BMI/SlicerPathology SlicerPathology extension source repository]
* [http://interactivemedical.org/imic2014/CameraReadyPapers/Paper%204/IMIC_ID4_FastGrowCut.pdf Fast Growcut]

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2016-01-08T04:55:00Z

Ebremer:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==


* Erich Bremer - [https://bmi.stonybrookmedicine.edu/ Stony Brook University]
* Yi Gao - [https://bmi.stonybrookmedicine.edu/ Stony Brook University]
* Nicole Aucoin - [http://www.brighamandwomens.org/ Brigham and Women's Hospital]
* Andrey Fedorov - [http://www.brighamandwomens.org/ Brigham and Women's Hospital]
* Kelli Xu - [http://www.mit.edu/ MIT]

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Create intuitive and user-friendly GUI
* make meta-data exportable
* Prepare extension for Phase II cloud work and future modules
|

* create work-flow module walking user through needed steps
* wrap editor module to allow for customization for segmentation purposes without interfering with global editor instance
* capture needed data elements and export them as [http://www.w3.org/TR/json-ld/ JSON-LD] supplementing exporting of masks
* augment GUI by requesting authentication information for [http://oauth.net/2/ OAuth 2.0] and adding elements for image selection via web.
* refactor existing extension modules into separate distinct editor effects modules (currently lumped as one)
|

* initial work-flow module created
* editor module wrapped and including in one of the step tabs of the work-flow module
* basic meta-data captured as part of label mask save
* username/password entries added to work-flow module for future web authentication
* original single editor-effect refactored into separate effects. Further cleaning of of code needed
* future work - allow image tiles to be select via web interface and resultant label masks and meta data to be exported directly to web services using OAuth2 authenication
|}

[[File:SlicerPathologybeginworkweek2016.png|600px|thumb|left|SlicerPathology extension at the start of Winter Work Week 2016]]
[[File:Afterworkweek.png|600px|thumb|left|SlicerPathology extension at the end of Winter Work Week 2016]]

==Background and References==


* [https://github.com/SBU-BMI/SlicerPathology SlicerPathology extension source repository]
* [http://interactivemedical.org/imic2014/CameraReadyPapers/Paper%204/IMIC_ID4_FastGrowCut.pdf Fast Growcut]

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2016-01-08T04:49:05Z

Ebremer: /* Project Description */

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==


* Erich Bremer - [https://bmi.stonybrookmedicine.edu/ Stony Brook University]
* Yi Gao - [https://bmi.stonybrookmedicine.edu/ Stony Brook University]
* Nicole Aucoin - [http://www.brighamandwomens.org/ Brigham and Women's Hospital]
* Andrey Fedorov - [http://www.brighamandwomens.org/ Brigham and Women's Hospital]
* Kelli Xu - [http://www.mit.edu/ MIT]

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Create intuitive and user-friendly GUI
* make meta-data exportable
* Prepare extension for Phase II cloud work and future modules
|

* create work-flow module walking user through needed steps
* wrap editor module to allow for customization for segmentation purposes without interfering with global editor instance
* capture needed data elements and export them as [http://www.w3.org/TR/json-ld/ JSON-LD] supplementing exporting of masks
* augment GUI by requesting authentication information for [http://oauth.net/2/ OAuth 2.0] and adding elements for image selection via web.
* refactor existing extension modules into separate distinct editor effects modules (currently lumped as one)
|

*
|}

[[File:SlicerPathologybeginworkweek2016.png|600px|thumb|left|SlicerPathology extension at the start of Winter Work Week 2016]]
[[File:Afterworkweek.png|600px|thumb|left|SlicerPathology extension at the end of Winter Work Week 2016]]

==Background and References==


* [https://github.com/SBU-BMI/SlicerPathology SlicerPathology extension source repository]
* [http://interactivemedical.org/imic2014/CameraReadyPapers/Paper%204/IMIC_ID4_FastGrowCut.pdf Fast Growcut]

File:Afterworkweek.png

2016-01-08T04:46:55Z

Ebremer:

2016 Winter Project Week/Breakout Session/What's Planned for Slicer Core

2016-01-07T17:00:21Z

Ebremer: /* Maintenance needed for core libraries */

=Introduction=
*Ron Kikinis: [http://wiki.na-mic.org/Wiki/images/e/ec/2015-11-11-Slicer-Status.pptx State of the Slicer world and strategic plans for Slicer]

=Maintenance needed for core libraries=
* VTK7 (rapid changes coming to VTK due to maintenance grant)
* Python: [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Labs/SlicerCondaIntegration conda] (and?)or cmake/wheels?
* Qt5: improvements, plus 4.8 may eventually stop supporting new systems
* support for latest WebKit

=Organization=
* Establish a mechanism to install multiple extension packages by default. Ron: I frequently download Slicer nightly build. Having to manually install the 10 packages that I need routinely is a pain. This will be a disincentive for me to download the nightly.
** would it be possible instead to recognize previous settings on the first launch of the new nightly, and ask user if s/he wants to re-install all or selection of the extensions installed before the update?
* Move modules to extension - See also [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DeprecatedModules Documentation/Labs/DeprecatedModules]
** Moving diffusion to extension
** Moving EMSegmenter to extension: very large, with lots of data; it would significantly reduce the Slicer installation package size
** Move BRAINS, SimpleITK, OpenIGTLinkIF to extension: frequently used modules but they are quite large, also by having them in extensions they could be updated without the need to create a new Slicer release
** Moving Endoscopy, PET SUV, various filters to extensions: small modules, they are just too specific to be included in the core
** ...other things to extensions?
* revise DICOM plugins organization - if the data is not recognized by installed plugins, there is no way for the user to know what extension to install to handle the dataset

Other suggestions:
* Keep official version of tier I extensions in GitHub in the Slicer organization so that any Slicer core developer can fix and update them easily.
* Move orphan extensions (that developers cannot maintain anymore) to GitHub under Slicer organization's ownership so that they can be kept in a working condition. See [http://na-mic.org/Mantis/view.php?id=2779 #2779]

=Key requests from the community=
* faster startup time (particularly mac). See http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/StartupTimeImprovement
* Less confusing UI
** Every module should be display an initial subset of the functionality (as minimal as possible) and a closed "Advanced" tab that contains everything else.
** cursor modes? http://www.na-mic.org/Bug/view.php?id=2419
** Slicer logo steals a lot of precious space - can we move it to the tools buttons toolbar? http://www.na-mic.org/Bug/view.php?id=3797
* Add orientation information to vtkImageData (request for VTK, not just Slicer but all VTK-based medical image computing groups suffer a lot because of this). See [https://github.com/SlicerRt/SlicerRT/blob/master/SegmentationCore/vtkOrientedImageData.h vtkOrientedImageData class] and [https://github.com/SlicerRt/SlicerRT/blob/master/SegmentationCore/vtkOrientedImageDataResample.h related utility]
* Make it easy to add custom slice and 3D widgets (for various custom quantification, segmentation, planning, targeting, etc. tasks - currently we can observe markup points and create custom models for visualization, but the method is very fragile and many things are missing, for example, no way to detect if the user clicks on a markup, no way to limit number of markups or restrict them to be placed on a certain surface, etc.)
* Modern, integrated revision control, issue tracking, dashboard, code review, documentation, etc. toolset
* Simplify data import/export/saving/loading (single-click save to database, direct data loading by drag-and-drop - by inspection of file contents instead of just checking file extension and asking the user how the data should be interpreted, automatic loading of just imported DICOM data, etc.)
* (add your favorites here...)

Some short-term but high-priority issues:
* GPU-based volume rendering (due to problem in VTK)
* Faster nightly builds (extensions appear in the extension manager too late for nightly builds)

Documentation and support
* improved integration of Slicer YouTube channel?
** What to do about China? http://slicer-devel.65872.n3.nabble.com/youtube-in-China-td4035615.html
* documentation page usage statistics to rank relevance of modules?
* discuss alternatives to mailing list?
** example from ITCR community (discussed at the ITCR Training and Outrech call, provided here from the meeting minutes by Andrey Fedorov)
*** https://support.bioconductor.org/
*** Bioconductor migrated their mailing list content to Biostars-based support forum site (modeled on stack overflow). Biostars is free and open source. Community core members were somewhat reluctant. Email list remains for technical/dev forum and support site is used for users. Email list is more like a back and forth dialogue. In contrast the support site has less back and forth. It’s made it easier for people to ask less knowledgeable questions.
*** Bioconductor recognizes individuals for their contributions to the support site.
*** Another factor in favor of the support site is that there is incentive nd motivation to contribute (upvotes, counts of # of responses, etc)

* improve outreach and visibility by being more "google friendly" ? http://www.na-mic.org/Bug/view.php?id=3938 Ron: how about China?

=Roadmaps=
*Steve Pieper: Chronicle, ctkjs, CommonGL
*JC Fillion-Robin: [http://girder.readthedocs.org/en/latest/ Girder], Anaconda, Factory machines
*Andras Lasso: [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/Sequences Sequences]
*Csaba Pinter: [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Segmentations Segmentations]
*Mike Halle: Slicer webinfrastructure and github
*Andrey Fedorov: DICOM objects for interoperability
** focus areas: segmentations, enhanced multiframe (single-file MR series, parametric maps), volumetric measurement structured reports
** approach
*** developer API in DCMTK
*** reusable command-line converters for extension developers
*** user-level domain-specific applications
** open question for discussion: should this functionality be in the core or extension

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2016-01-03T15:54:34Z

Ebremer:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==


* Erich Bremer - [https://bmi.stonybrookmedicine.edu/ Stony Brook University]
* Yi Gao - [https://bmi.stonybrookmedicine.edu/ Stony Brook University]
* Nicole Aucoin - [http://www.brighamandwomens.org/ Brigham and Women's Hospital]
* Andrey Fedorov - [http://www.brighamandwomens.org/ Brigham and Women's Hospital]

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Create intuitive and user-friendly GUI
* make meta-data exportable
* Prepare extension for Phase II cloud work and future modules
|

* create work-flow module walking user through needed steps
* wrap editor module to allow for customization for segmentation purposes without interfering with global editor instance
* capture needed data elements and export them as [http://www.w3.org/TR/json-ld/ JSON-LD] supplementing exporting of masks
* augment GUI by requesting authentication information for [http://oauth.net/2/ OAuth 2.0] and adding elements for image selection via web.
* refactor existing extension modules into separate distinct editor effects modules (currently lumped as one)
|

*
|}

[[File:SlicerPathologybeginworkweek2016.png|600px|thumb|left|SlicerPathology extension at the start of Winter Work Week 2016]]

==Background and References==


* [https://github.com/SBU-BMI/SlicerPathology SlicerPathology extension source repository]
* [http://interactivemedical.org/imic2014/CameraReadyPapers/Paper%204/IMIC_ID4_FastGrowCut.pdf Fast Growcut]

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2016-01-03T15:53:41Z

Ebremer:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==


* Erich Bremer - [https://bmi.stonybrookmedicine.edu/ Stony Brook University]
* Yi Gao - [https://bmi.stonybrookmedicine.edu/ Stony Brook University]
* Nicole Aucoin - [http://www.brighamandwomens.org/ Brigham and Women's Hospital]
* Andrey Fedorov - [http://www.brighamandwomens.org/ Brigham and Women's Hospital]

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Create intuitive and user-friendly GUI
* make meta-data exportable
* Prepare extension for Phase II cloud work and future modules
|

* create work-flow module walking user through needed steps
* wrap editor module to allow for customization for segmentation purposes
* capture needed data elements and export them as [http://www.w3.org/TR/json-ld/ JSON-LD] supplementing exporting of masks
* augment GUI by requesting authentication information for [http://oauth.net/2/ OAuth 2.0] and adding elements for image selection via web.
* refactor existing extension modules into separate distinct editor effects modules (currently lumped as one)
|

*
|}

[[File:SlicerPathologybeginworkweek2016.png|600px|thumb|left|SlicerPathology extension at the start of Winter Work Week 2016]]

==Background and References==


* [https://github.com/SBU-BMI/SlicerPathology SlicerPathology extension source repository]
* [http://interactivemedical.org/imic2014/CameraReadyPapers/Paper%204/IMIC_ID4_FastGrowCut.pdf Fast Growcut]

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2016-01-03T15:51:56Z

Ebremer:

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2016-01-03T15:50:17Z

Ebremer:

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2016-01-03T15:49:31Z

Ebremer:

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2015-12-29T16:22:19Z

Ebremer:

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2015-12-29T16:20:23Z

Ebremer:

File:SlicerPathologybeginworkweek2016.png

2015-12-29T16:19:26Z

Ebremer:

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2015-12-29T16:17:09Z

Ebremer:

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2015-12-29T16:15:53Z

Ebremer:

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2015-12-29T16:15:13Z

Ebremer:

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2015-12-29T16:13:44Z

Ebremer:

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2015-12-29T16:12:49Z

Ebremer:

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2015-12-29T16:10:07Z

Ebremer:

2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation

2015-12-29T16:07:53Z

Ebremer:

2016 Winter Project Week

2015-12-29T15:59:27Z

Ebremer: adding an author or SlicerPathology extension

__NOTOC__
[[image:PW-MIT2016.png|300px]]

'''Dates:''' January 4-8, 2016

'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)

'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here].
 

== Introduction ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a [http://www.miccai.org/organization MICCAI] endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 4
!style="width:18%" |Tuesday, January 5
!style="width:18%" |Wednesday, January 6
!style="width:18%" |Thursday, January 7
!style="width:18%" |Friday, January 8
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|'''10:30am-12pm:''' [Tutorial] Diffeomorphic registration and geodesic shooting methods (I). (Sarang Joshi) Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10:00-11:30am:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/NewSlicerExtensions | Slicer Extensions Birds of a Feather]]
|
'''10:00-11:30am:''' Breakout Session: [[2016_Winter_Project_Week/Projects/SlicerROSIntegration| Slicer for Medical Robotics Research]]
 
|'''8:30-9:30am''' TBD 
'''9:30-10:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Image-guided Neurosurgery| Clinical perspective on Image Guided Neurosurgery]] (Alexandra Golby) 
'''10:30-11:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Multiparametric MRI| Clinical perspective on Multiparametric MRI]] (Fiona Fennessy) 
'''11:30am-12:30pm''' TBD 
|'''10:00am-12:00pm:''' [[#Projects|Project Progress Updates]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ----------------- 
'''12pm:''' [[Events:TutorialContestJanuary2016|Tutorial Contest Winner Announcement]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1:00-5:30pm'''
|'''1:00pm-1:05pm: Welcome''' 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ----------------- 
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads) 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ----------------- 
'''2:45-4:00pm:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Ultrasound]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ----------------- 

'''4:00-5:30pm:''' [Tutorial] Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi) Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|
|'''1:00-2:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/DiffusionMRI| Diffusion MRI]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]] 
'''3:00-4:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/QIICRTools| QIICR Tools]]
|'''1:00-3:00pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20160103%2F20160110
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20160103/20160110
}}

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

='''Projects'''=
*Use this [[2016_Project_Week_Template | Updated Template for project pages]]

== Tractography==
* [[2016_Winter_Project_Week/Projects/Tractography_format_interoperability | Tractography Format Interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/SlicerDMRI_documentation | Slicer Diffusion MR / tractography workflow documentation]] (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/TractographyModuleDevelop&Test | Tractography Analysis Module Development and Testing]] (Fan Zhang, Pegah Kahaliardabili, Isaiah Norton, Lauren O'Donnell, others)

== IGT ==
* [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/IntegrationCustusX|Integration of CustusX with PLUS on BK System]] (Christian A, Andras Lasso, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
*[[2016_Winter_Project_Week/Projects/IntegrationImFusion| Integration of ImFusion MR-US Registration with BWH AMIGO Neurosurgery Setup]] (Sarah Frisken, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso, Christian Askelan)
* [[2016_Winter_Project_Week/Projects/SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard, Jayender Jagadeesan)
* [[2016_Winter_Project_Week/Projects/CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)
* [[2016_Winter_Project_Week/Projects/External_beam_planning | External Beam Radiotherapy Planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week/Projects/EVD |Measuring Anatomic Factors for Extraventricular Drain Placement]] (Kirby Vosburgh, P. Jason White)
* [[2016_Winter_Project_Week/Projects/PLUS | Inter-device messaging for robust support of depth switching]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/PLUSOCR | Exploration of open-source OCR libraries for device meta-data capture without research interface ]] (Adam Rankin)

==Image Analysis==
*[[2016_Winter_Project_Week/Projects/ChestImagingPlatform|Chest Imaging Platform: COPD and Other Pulmonary Diseases]] (Raúl San José, Jorge Onieva)
* [[2016 Winter Project Week/Projects/Cluster-Driven Lung Segmentation | Cluster-Driven Segmentation of Lung Nodules]] (Vivek Narayan, Raúl San José, Daniel Blezek, Steve Pieper, Chintan Parmar)
* [[2016_Winter_Project_Week/Projects/BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week/Projects/ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week/Projects/PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
*[[2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation|Digital Pathology Nuclear Segmentation]] (Erich Bremer, Yi Gao, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/Interactive4DSegmentation | Interactive 4D Segmentation Module]] (Ethan Ulrich)
* [[2016_Winter_Project_Week/Projects/SlicerCMFNextSteps | Moving beyond SlicerCMF and Future Projects]] (Beatriz Paniagua, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/ShapeAnalysis | Low-dimensional Principal Geodesic Analysis On the Manifold of Diffeomorphisms]] (Miaomiao Zhang, Polina Golland)

==Infrastructure==
*[[2016_Winter_Project_Week/Projects/UpgradeNAMICSlicerWiki|Upgrade the NAMIC (and Slicer?) Wiki]] (Mike Halle, JC)
* [[2016_Winter_Project_Week/Projects/CommonDataStructure | Common Data Structure for CMF modules in Slicer]] (Jean-Baptiste Vimort, François Budin, Lucia Cevidanes, Beatriz Paniagua, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/StatisticalShapeModeling | Statistical Shape Modeling in Slicer: OA Index]] (Laura Pascal, Beatriz Paniagua, François Budin, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week/Projects/CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab Asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week/Projects/BRAINSFit_in_MeVisLab | Interoperability Tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week/Projects/CLI_Dashboard | Kibana Dashboard for Browsing All Available CLI Modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week/Projects/SegmentationEditorWidget | Editor Widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week/Projects/SlicerTerminologyEditor | Terminology Editor]] (Csaba Pinter, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/DICOMSegObjIntegration | Integration of DICOM Segmentation Image Storage with Segmentations Module]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week/Projects/CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week/Projects/Data Persisting | Mechanism to Persist Clinical User Data from Different Modules Based on SQLite and/or other Database Engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/Workflows | Workflow Module that Enables the Navigation and Data Sharing between Different Modules in a Clinical Workflow ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/AIMInteroperability | AIM for Interoperability]] (Hans Meine, Andrey Fedorov, ??)
* [[2016_Winter_Project_Week/Projects/3DNrrdSequences | Sequences extension support for 3D+t NRRD]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/SlicerEnhancedMR | Developing support for Enhanced MR in Slicer]] (Michael Onken, Andrey Fedorov)

= '''Logistics''' =

*'''Dates:''' January 4-8, 2016
*'''Location:''' MIT, Kiva Conference room; 4th floor of Building 32.
*'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here]. Registration Fee: $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list [[2016_Winter_Project_Week/RoomSharing|here]]

= '''Registrants''' =

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/namic16 registration site].

#Polina Golland, MIT
#Ron Kikinis, BWH
#Nicole Aucoin, BWH/SPL
#Peter Anderson
#Daniel Blezek, Isomics, Inc.
#Lucia Cevidanes, University of Michigan
#Adrian Dalca, MIT
#Simon Drouin, Montreal Neurological Institute
#Janek Groehl, German Cancer Research Center
#Tina Kapur, BWH/HMS
#Thomas Kirchner, German Cancer Research Center
#Hans Meine, University of Bremen/MEVIS
#Vivek Narayan, Dana Farber Cancer Institute
#Danielle Pace, MIT
#Laura Pascal, University of Michigan
#Steve Pieper, Isomics, Inc.
#Csaba Pinter, Queen's University
#Gregory Sharp, MGH
#James Miller, GE Research
#Kyle Sunderland, Queen's University
#Ethan Ulrich, University of Iowa
#Jean-Baptiste Vimort, University of Michigan
#Miaomiao Zhang, MIT
#Beatrize Paniagua, University of North Carolina at Chapel Hill
#Sonia Pujol, BWH
#Junichi Tokuda, BWH
#Katie Mastrogiacomo, BWH
#Niravkumar Patel, Worcester Polytechnic Institute
#Michael Onken, Open Connections (Germany)
#Erich Bremer, Stony Brook University
#Xiao Da, MGH
#Tobias Frank, Leibniz Universität Hannover
#Kirby Vosburgh, BWH
#P. Jason White, BWH
#Lauren O'Donnell, BWH
#Pegah Kahali, BWH
#Fan Zhang, BWH
#Adam Rankin, Robarts Research Institute
#Simon Leoard, Johns Hopkins University
#David Gering, HealthMyne
#Johan Andruejol, Kitware
#Jean-Christophe Fillion-Robin, Kitware
#Kelly Xu, MIT
#Christian Askeland, SINTEF
#Katharine Carter, BWH
#Nick Todd, BWH
#Ye Cheng, BWH
#Andriy Fedorov, BWH/HMS
#Sudhanshu Semwal, UCCS Professor
#Michael Halle, BWH