2016 Winter Project Week

Dates: January 4-8, 2016

Location: MIT, Cambridge, MA. (Rooms: Kiva, R&D)

REGISTRATION: Register 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 NCBC program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform 3D Slicer, built using VTK, ITK, CMake, and 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.

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 NAC, NCIGT, QIICR, and OCAIRO.

A summary of all previous Project Events is available here.

This project week is an event endorsed by the MICCAI society.

Please make sure that you are on the na-mic-project-week mailing list

Agenda

Tentative Agenda

Time	Monday, January 4	Tuesday, January 5	Wednesday, January 6	Thursday, January 7	Friday, January 8
	Project Presentations			IGT Day	Reporting Day
8:30am		Breakfast	Breakfast	Breakfast	Breakfast
9:00am-12:00pm	10:30am-12pm: Tutorial: Diffeomorphic registration and geodesic shooting methods (I). (Sarang Joshi) Room: 32-D507.	10:00-11:30am: Breakout Session: New Slicer Extensions	10:00-11:30am: Breakout Session: Slicer for Medical Robotics Research	9:00-10:30am TBD ----------------- 10:00am-12:00pm: Breakout Session: TBD	10:00am-12:00pm: Project Progress Updates Kiva ----------------- 12pm: Tutorial Contest Winner Announcement Kiva
12:00pm-1:00pm	Lunch	Lunch	Lunch	Lunch	Lunch boxes; Adjourn by 1:30pm
1:00-5:30pm	1:00pm-1:05pm: Welcome Kiva ----------------- 1:05-2:30pm: Project Introductions (all Project Leads) Kiva ----------------- 2:45-4:00pm: Breakout Session: Ultrasound Kiva ----------------- 4:00-5:30pm: Tutorial: Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi) Room: 32-D507.		1:00-2:30pm: Breakout Session: Diffusion MRI Kiva 3:00-4:30pm: Breakout Session: QIICR Tools	1:00-3:00pm: Breakout Session: What's Planned for Slicer Core Kiva
5:30pm	Adjourn for the day	Adjourn for the day	Adjourn for the day	Adjourn for the day

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Projects

• Use this 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)
• Batch Clinical Image Analysis (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
• Image Restoration via Patch GMMs (Adrian Dalca, Katie Bouman, Polina Golland)
• Patch Based Discrete Registration for Difficult Images (Adrian Dalca, Andreea Bobu, Polina Golland)
• External beam radiotherapy planning (Greg Sharp, others)
• Slicer OpenCV Extension (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
• Common data structure for CMF modules in Slicer (Jean-Baptiste Vimort, François Budin, Lucia Cevidanes, Beatriz Paniagua, Steve Pieper, Juan Prieto)
• Statistical Shape Modeling in Slicer: OA Index (Laura Pascal, Beatriz Paniagua, François Budin, Lucia Cevidanes, Steve Pieper, Juan Prieto)
• Moving beyond SlicerCMF and future projects (Beatriz Paniagua, Lucia Cevidanes, Steve Pieper, Juan Prieto)
• Tractography format interoperability (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
• Slicer diffusion MR / tractography workflow documentation (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)
• Cluster-Driven Segmentation of Lung Nodules (Vivek Narayan, Raúl San José, Daniel Blezek, Steve Pieper, Chintan Parmar)

IGT

• 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)
• 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)
• 3D Slicer + ROS Integration (Junichi Tokuda, Axel Krieger, Simon Leonard)
• CryoPlanning Module in Slicer (Jayender Jagadeesan, Steve Pieper, Sandy Wells)

Infrastructure

• CommonGL (Steve Pieper, Jim Miller)
• Running CLI Modules in MeVisLab asynchronously (Hans Meine)
• Interoperability tests with BRAINSFit (or other interesting CLIs) in MeVisLab (Hans Meine, Steve Pieper)
• Kibana dashboard for browsing all available CLI modules (Hans Meine, JC?)
• Editor widget using Segmentations (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
• Terminology Editor (Csaba Pinter, Nicole Aucoin, Andrey Fedorov)
• Integration of DICOM segmentation image storage with Segmentations module (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
• Integration of Anaconda Python in Slicer (JC, Raúl San José, Jorge Onieva, Slicer Community?)
• Mechanism to persist clinical user data from different modules based on SQLite and/or other database engines (Raúl San José, Jorge Onieva)
• Workflow module that enables the navigation and data sharing between different modules in a clinical workflow (Raúl San José, Jorge Onieva)
• 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 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 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 registration site.

1. Polina Golland, MIT
2. Ron Kikinis, BWH
3. Nicole Aucoin, BWH/SPL
4. Peter Anderson
5. Daniel Blezek, Isomics, Inc.
6. Lucia Cevidanes, University of Michigan
7. Adrian Dalca, MIT
8. Simon Drouin, Montreal Neurological Institute
9. Janek Groehl, German Cancer Research Center
10. Tina Kapur, BWH/HMS
11. Thomas Kirchner, German Cancer Research Center
12. Hans Meine, University of Bremen/MEVIS
13. Vivek Narayan, Dana Farber Cancer Institute
14. Danielle Pace, MIT
15. Laura Pascal, University of Michigan
16. Steve Pieper, Isomics, Inc.
17. Csaba Pinter, Queen's University
18. Gregory Sharp, MGH
19. Kyle Sunderland, Queen's University
20. Ethan Ulrich, University of Iowa
21. Jean-Baptiste Vimort, University of Michigan
22. Miaomiao Zhang, MIT
23. Beatrize Paniagua, University of North Carolina at Chapel Hill
24. Sonia Pujol, BWH
25. Junichi Tokuda, BWH
26. Michael Onken, Open Connections (Germany)
27. Eric Bremer, Stony Brook University
28. Xiao Da, MGH
29. Tobias Frank, Leibniz Universität Hannover
30. Kirby Vosburgh, BWH
31. P. Jason White, BWH