NAMIC Wiki - User contributions [en]

2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data

2017-01-13T15:11:06Z

Mirclem:

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

</gallery>

==Key Investigators==

* Juan Carlos Prieto (University of North Carolina)
* Clément Mirabel (University of Michigan)

==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;"
|

* Allow users to store online the data they use for their studies, with the possibility to share their data with other projects to have bigger datasets.
* Develop a Slicer module to ease the upload of morphological (imaging) data.
* Federate different statistics tools and facilitate their use for project managers.
* Help project managers to know the progression of their project and collection of their data with visual graphs.
|

* Have user feedback about the Slicer module.
* Integrate R functions in the server to do statistical analysis with imaging data and biological data.
* Add functionalities to facilitate the use of the website to clinicians.
|

* Talks about existing other web projects. We gave demos and had feedbacks.
* We added few scripts on a remote server to be run directly from Slicer.
* We were able to train a neural network giving a dataset in Slicer, then enter an input shape and have a classification result.
|}

==Background and References==

[https://ec2-52-42-49-63.us-west-2.compute.amazonaws.com:8180/DCBIA-OrthoLab/public/# Website URL] 
[https://github.com/DCBIA-OrthoLab/shiny-tooth Website source code] 
[https://github.com/DCBIA-OrthoLab/DatabaseInteractorExtension Slicer module source code]

2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data

2017-01-13T15:09:17Z

Mirclem:

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

</gallery>

==Key Investigators==

* Juan Carlos Prieto (University of North Carolina)
* Clément Mirabel (University of Michigan)

==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;"
|

* Allow users to store online the data they use for their studies, with the possibility to share their data with other projects to have bigger datasets.
* Develop a Slicer module to ease the upload of morphological (imaging) data.
* Federate different statistics tools and facilitate their use for project managers.
* Help project managers to know the progression of their project and collection of their data with visual graphs.
|

* Have user feedback about the Slicer module.
* Integrate R functions in the server to do statistical analysis with imaging data and biological data.
* Add functionalities to facilitate the use of the website to clinicians.
|

* Talks about existing other web projects. We gave demos and had feedbacks.
* We added few scripts on a remote server to be run directly from Slicer. We were able to train a network giving a dataset in Slicer, then enter an input shape and have a classification result.
|}

==Background and References==

[https://ec2-52-42-49-63.us-west-2.compute.amazonaws.com:8180/DCBIA-OrthoLab/public/# Website URL] 
[https://github.com/DCBIA-OrthoLab/shiny-tooth Website source code] 
[https://github.com/DCBIA-OrthoLab/DatabaseInteractorExtension Slicer module source code]

2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data

2016-12-19T16:15:49Z

Mirclem: /* Background and References */

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

</gallery>

==Key Investigators==

* Juan Carlos Prieto (University of North Carolina)
* Clément Mirabel (University of Michigan)

==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;"
|

* Allow users to store online the data they use for their studies, with the possibility to share their data with other projects to have bigger datasets.
* Develop a Slicer module to ease the upload of morphological (imaging) data.
* Federate different statistics tools and facilitate their use for project managers.
* Help project managers to know the progression of their project and collection of their data with visual graphs.
|

* Have user feedback about the Slicer module.
* Integrate R functions in the server to do statistical analysis with imaging data and biological data.
* Add functionalities to facilitate the use of the website to clinicians.
|

*
|}

==Background and References==

[https://ec2-52-42-49-63.us-west-2.compute.amazonaws.com:8180/DCBIA-OrthoLab/public/# Website URL] 
[https://github.com/DCBIA-OrthoLab/shiny-tooth Website source code] 
[https://github.com/DCBIA-OrthoLab/DatabaseInteractorExtension Slicer module source code]

2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data

2016-12-19T16:00:32Z

Mirclem: 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..."

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

</gallery>

==Key Investigators==

* Juan Carlos Prieto (University of North Carolina)
* Clément Mirabel (University of Michigan)

==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;"
|

* Allow users to store online the data they use for their studies, with the possibility to share their data with other projects to have bigger datasets.
* Develop a Slicer module to ease the upload of morphological (imaging) data.
* Federate different statistics tools and facilitate their use for project managers.
* Help project managers to know the progression of their project and collection of their data with visual graphs.
|

* Have user feedback about the Slicer module.
* Integrate R functions in the server to do statistical analysis with imaging data and biological data.
* Add functionalities to facilitate the use of the website to clinicians.
|

*
|}

==Background and References==

2017 Winter Project Week

2016-12-19T15:33:24Z

Mirclem:

__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)

== Robotics in IGT ==
* [[2017 Winter Project Week/OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab | OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab ]] (Scheherazade Kraß (Shery), Junichi Tokuda, Longquan Chen, )

== Craniofacial ==
* [[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)

== 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