2017 Winter Project Week

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 Tina Kapur, PhD.

Logistics

• Dates: January 9-13, 2017.
• Location: MIT CSAIL, Cambridge, MA. (Rooms: Kiva, R&D)
• Transportation: Public transportation is highly encouraged, as no parking permits will be issued by MIT. For a list of local garages, please see here
• REGISTRATION: Register here. Registration Fee: $330.
• Hotel: Similar to previous years, no rooms have been blocked in a particular hotel.
• Next Project Week:' June 26-30, 2017, Catanzaro, Italy

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 NCBC program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform 3D Slicer, enhancements to the underlying building blocks 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 open source hackathon event called Project Week.

Project Week is a semi-annual open source hackathon which draws 60-120 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.

Please make sure that you are on the NA-MIC Project Week mailing list

Conference Calls for Preparation

Conference call phone number and notes are available here.

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.

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

Projects

• Use this Updated Template for project pages

Learning and GPUs

1. Needle Segmentation from MRI (Ziyang Wang, Guillaume Pernelle, Paolo Zaffino, Tina Kapur)
2. Deep Learning for Synthetic MRI (Frank Preiswerk, Yaofei "Ada" Wang)
3. An open-source tool to classify TMJ OA condyles (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)
4. DeepInfer: Open-source Deep Learning Deployment Toolkit (Alireza Mehrtash, Mehran Pesteie, Yang (Silvia) Yixin, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)
5. Evaluate Deep Learning for binary cancer lesion classification (Curt Lisle)

Web Technologies

Web Technology and Slicer (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)

1. Slicer Qt5 and Python3 (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
2. OAuth2.0 authentication in SlicerPathology (Erich Bremer, Steve Pieper)
3. Explore integration of Web-based imaging workflows with Slicer (Curt Lisle, Satra Gosh, Steve Peiper)
4. IPFS and NoSQL for cloud databases (Hans Meine, Steve Pieper)
5. Web-based system to federate biological, clinical and morphological data (Juan Carlos Prieto, Clément Mirabel)
6. Electron App to add, navigate and visualize DICOM images (Smruti Padhy, Satrajit Ghosh, Mathias Goncalves)

IGT: Navigation, Robotics, Surgical Planning

• Tracked Ultrasound Standardization III: The Refining (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
• ROS Surface Scan (Tobias Frank, Junichi Tokuda, Longquan Chen)
• Open Source Electromagnetic Trackers (Peter Traneus Anderson)
• OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab (Scheherazade Kraß (Shery), Junichi Tokuda, Longquan Chen, )
• Liver resection planning extension (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
• Prostate Gland Sector Segmentation (Anneke Meyer, Andrey Fedorov)
• Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery (Jennifer Nitsch)
• Segmentation of meningiomas in structural MR images (Satrajit Ghosh, Omar Arnaout)
• Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging (Haoyin Zhou, Jayender Jagadeesan)

dMRI

• WhiteMatterAnalysis New Module and Documentation (Fan Zhang, Shun Gong, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)
• Density-based DMRI registration (Henrik Groenholt Jensen, Lauren J. O'Donnell, Tina Kapur, Fan Zhang, Carl-Fredrik Westin)
• SlicerDMRI Testing and Documentation (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)
• DiPy integration in Slicer (Isaiah Norton, Lauren J. O'Donnell)
• Identification of information-rich patches in Diffusion-Weighted Images (Laurent Chauvin, Fan Zhang, Lauren J. O'Donnell, Matthew Toews)

Quantitative Imaging Informatics

• dcmqi library and DICOM QuantitativeReporting (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
• PyRadiomics library (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)

Visualization

• Slicer & HoloLens (Adam Rankin, Andras Lasso)

Infrastructure

• Subject hierarchy single-node refactoring (Csaba Pinter)
• Slicer support for interactive modification of 3D models (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
• PkModeling - DCE Modeling Accuracy and UI/UX Update (Andrew Beers)
• Manual Segmentation Module w/ Subtraction Maps + Delaunay Models (Andrew Beers)
• Updating Community Forums (Discourse, GitHub, Gitter, ???) (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)
• Support for volumetric meshes (Alexis Girault, Curtis Lisle, Steve Piper)
• Improve Matlab integration (Alexis Girault, Andras Lasso)

To be Categorized

• Slicer for Hyperspectral Ophthalmology Analysis (Sungmin Hong)
• Slicer for Shape Analysis (Beatriz Paniagua)
• Mandibular Shape Regression (Beatriz Paniagua, James Fishbaugh)
• Upgrade Plastimatch extension (Greg Sharp)
• Tutorial contest (Sonia Pujol)
• Geodesic Segmentation and Lung tumor Analysis (Patmaa S, Sarthak Pati, Ratheesh k, Mark B, Yong F, Despina K, Ragini V, Christos D)

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. A, Zeina :: SHBOUL
2. Aerts, Hugo :: DFCI-Harvard
3. Alam, Mahbubul :: Old Dominion University
4. Anderson, Peter :: Retired
5. Andruejol, Johan :: Kitware, Inc.
6. Bakeng, Janne Beate :: SINTEF
7. Beers, Andrew :: Massachusetts General Hospital
8. Bernal Rusiel, Jorge Luis :: Boston Children's Hospital
9. Bremer, Erich :: Stony Brook University
10. Burke, Brice :: American University of Antigua College of Medicine
11. Cetin Karayumak, Suheyla :: Brigham and Women's Hospital
12. Chae, Michael :: Monash University
13. Chauvin, Laurent :: ETS
14. Dalca, Adrian :: Massachusetts Institute of Technology
15. Fedorov, Andriy :: Brigham and Women's Hospital
16. Fillion-Robin, Jean-Christophe :: Kitware, Inc.
17. Fishbaugh, James :: New York University
18. Frank, Tobias :: Leibniz Universität Hannover
19. García Mato, David :: Queen´s University / Universidad Carlos III de Madrid
20. Girault, Alexis :: Kitware, Inc.
21. Golland, Polina :: Massachusetts Institute of Technology
22. Gollub, Randy :: Massachusetts General Hospital
23. Gong, Shun :: Brigham and Women's Hospital
24. Guerrier de Dumast, Priscille :: University of Michigan
25. Harris, Gordon :: Massachusetts General Hospital
26. Herz, Christian :: Brigham and Women's Hospital
27. Hong, Sungmin :: New York University
28. Hosny, Ahmed :: Dana-Farber
29. Jagadeesan, Jayender :: Brigham and Women's Hospital
30. Jensen, Henrik G. :: University of Copenhagen
31. Kapur, Tina :: Brigham and Women's Hospital
32. Kikinis, Ron :: Brigham and Women's Hospital
33. Lasso, Andras :: PerkLab, Queen's University
34. Lauer, Rebekka :: Humboldt University Berlin
35. Lisle, Curtis :: KnowledgeVis, LLC
36. Mastrogiacomo, Katie :: Brigham and Women's Hospital
37. Mateus, D. :: TUM
38. Mehrtash, Alireza :: Brigham and Women's Hospital
39. Meine, Hans :: University of Bremen
40. Meyer, Anneke :: University of Magdeburg
41. Miller, James :: GE Research
42. Mirabel, Clement :: University of Michigan
43. Nitsch, Jennifer :: University of Bremen
44. Norton, Isaiah :: Brigham and Women's Hospital
45. O'Donnell, Lauren :: Brigham and Women's Hospital
46. Oram, Louise :: The Intervention Centre-Oslo University Hospital
47. Paniagua, Beatriz :: Kitware, Inc.
48. Parmar, Chintan :: DFCI-Harvard Medical School
49. Peled, Sharon :: Brigham and Women's Hospital
50. Pieper, Steve :: Isomics, Inc.
51. Pinter, Csaba :: Queen's University
52. Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School
53. Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School
54. Rankin, Adam :: Robarts Research Institute
55. Rheault, Francois :: Université de Sherbrooke
56. Roethe, Anna :: Humboldt University / Charité University Hospital Berlin
57. Sharp, Gregory :: Massachusetts General Hospital
58. Sridharan, Patmaa :: University of Pennsylvania-CBICA
59. Vidyaratne, Lasitha :: Old Dominion University
60. Wang, Yaofei :: Brigham and Women's Hospital
61. Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School
62. Yang, Yixin :: Brigham and Women's Hospital
63. Ye, Wu :: Brigham and Women's Hospital
64. Zaffino, Paolo :: Magna Graecia University of Catanzaro, Italy
65. Zeleznik, Roman :: DFCI
66. Zhang, Fan :: Brigham and Women's Hospital
67. Zhang, Miaomiao :: Massachusetts Institute of Technology
68. Zhang, Yuqian :: Brigham and Women's Hospital
69. Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital