2017 Winter Project Week

2016-12-29T20:48:14Z

Elizucker: /* Registrants */

2017 Winter Project Week

2016-12-19T19:16:12Z

Elizucker: /* Registrants */

2017 Winter Project Week

2016-12-13T22:28:46Z

Elizucker: /* Registrants */

2015-12-14T17:06:33Z

Elizucker: /* Registrants */

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

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

'''Location:''' MIT, 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 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==

Tentative 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"|'''9am-12pm'''
|'''10:30am-12pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 1 by Sarang Joshi) Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10-11:30am:''' Breakout Session: New Slicer Extensions''' 
|
'''10-11:30am:''' Breakout Session: [[2015_Winter_Project_Week:SlicerROSIntegration| Slicer for Medical Robotics Research]] 
 
|'''9:00-10:30am''' TBD 
 ---------------------------------------- 
'''10am-12pm: Breakout Session:''' TBD 
|'''10am-12pm:''' [[#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"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: Welcome''' 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads) 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 
'''2:45-4pm:''' [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Breakout Session Ultrasound]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 

'''4:00pm-5:30pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 2 by Sarang Joshi) Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''1-3pm:''' [[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' Breakout Session:''' [[2016_Winter_Project_Week/Breakout_Sessions/Diffusion MRI| Diffusion MRI]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]] -------- 
'''3-4:30pm:''' Breakout Session:''' [[2016_Winter_Project_Week/Breakout_Sessions/QIICR Tools| QIICR Tools]]
|
|
|-
|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
|
|}
<googlecalendar>kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com</googlecalendar>

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

== Non-categorized ==
*Digital Pathology Nuclear Segmentation (Erich Bremer, Nicole Aucoin, Andrey Fedorov)
*Chest Imaging Platform: COPD and other pulmonary diseases (Raúl San José, Jorge Onieva)
*Upgrade the namic (and Slicer?) wiki (JC, Mike Halle)
* [[2016_Winter_Project_Week:BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week:ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week:PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week:External_beam_planning | External beam radiotherapy planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week:SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week:CommonDataStructure | Common data structure for CMF modules in Slicer]] (Françoi Budin, Lucia Cevidanes, Beatriz Paniagua, Steeve Pieper, Juan Carlos Prieto, Jean-Baptiste Vimort)
* [[2016_Winter_Project_Week:Tract_io_interop | Tractography format interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week:SlicerDMRI_documentation | Slicer diffusion MR / tractography workflow documentation]] (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)

== IGT ==
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*Integration of CustusX with PLUS on BK System (Christian A, Adam Rankin)
* [[2016_Winter_Project_Week:MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
*Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup (Christian A, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso)
* [[2015_Winter_Project_Week:SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)

==Infrastructure==
* [[2016_Winter_Project_Week:CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week:WebTechnologies | Web Technologies and Slicer]] (Steve Pieper, Hans Meine)
* [[2016_Winter_Project_Week:CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week:CLI_Dashboard | Kibana dashboard for browsing all available CLI modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week:SegmentationEditorWidget | Editor widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:SlicerTerminologyEditor | Terminology Editor]] (Csaba Pinter, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week:DICOMSegObjIntegration | Integration of DICOM segmentation image storage with Segmentations module]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week: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: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:AIMInteroperability | AIM for interoperability]] (Hans Meine, 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 [https://www.regonline.com/namic16 this registration url].

Polina Golland, MIT
Ron Kikinis, BWH