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

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

IGT: Navigation, Robotics, Surgical Planning

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

dMRI

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

Quantitative Imaging Informatics

1. dcmqi library and DICOM QuantitativeReporting (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
2. PyRadiomics library (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)
3. PkModeling - DCE Modeling Accuracy and UI/UX Update (Andrew Beers)
4. Manual Segmentation Module w/ Subtraction Maps + Delaunay Models (Andrew Beers)

Visualization

1. Slicer & HoloLens (Adam Rankin, Andras Lasso)

Infrastructure

1. Subject hierarchy single-node refactoring (Csaba Pinter)
2. Slicer support for interactive modification of 3D models (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
3. Updating Community Forums (Discourse, GitHub, Gitter, ???) (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)
4. Support for volumetric meshes (Alexis Girault, Curtis Lisle, Steve Piper)
5. Improve Matlab integration (Alexis Girault, Andras Lasso)
6. Upgrade Plastimatch extension (Greg Sharp)

Shape Analysis

1. Slicer for Shape Analysis (Beatriz Paniagua)
2. Mandibular Shape Regression (Beatriz Paniagua, James Fishbaugh)

To be Categorized

1. Slicer for Hyperspectral Ophthalmology Analysis (Sungmin Hong)
2. Geodesic Segmentation and Lung tumor Analysis (Patmaa S, Sarthak Pati, Ratheesh k, Mark B, Yong F, Despina K, Ragini V, Christos D)
3. Tutorial contest (Sonia Pujol)

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. Aman Shboul, Zaina :: Old Dominion University
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. Drouin, Simon :: Montreal Neurological Institute
16. Fan, Zhipeng :: Brigham and Women's Hospital
17. Fedorov, Andriy :: Brigham and Women's Hospital
18. Fillion-Robin, Jean-Christophe :: Kitware, Inc.
19. Fishbaugh, James :: New York University
20. Frank, Tobias :: Leibniz Universität Hannover
21. Frisken, Sarah :: Brigham and Women's Hospital
22. García Mato, David :: Queen´s University / Universidad Carlos III de Madrid
23. Ghafoorian, Mohsen :: Brigham and Women's Hospital
24. Ghosh, Satrajit :: Massachusetts Institute of Technology
25. Girault, Alexis :: Kitware, Inc.
26. Golland, Polina :: Massachusetts Institute of Technology
27. Gollub, Randy :: Massachusetts General Hospital
28. Goncalves, Mathias :: Massachusetts Institute of Technology
29. Gong, Shun :: Brigham and Women's Hospital
30. Guerrier de Dumast, Priscille :: University of Michigan
31. Harris, Gordon :: Massachusetts General Hospital
32. Helba, Brian :: Kitware, Inc.
33. Herz, Christian :: Brigham and Women's Hospital
34. Hong, Sungmin :: New York University
35. Hosny, Ahmed :: Dana-Farber
36. Jagadeesan, Jayender :: Brigham and Women's Hospital
37. Jarecka, Dorota :: Massachusetts Institute of Technology
38. Jensen, Henrik G. :: University of Copenhagen
39. Kaczmarzyk, Jakub :: Massachusetts Institute of Technology
40. Kapur, Tina :: Brigham and Women's Hospital
41. Kennedy, David :: UMass Medical School
42. Kikinis, Ron :: Brigham and Women's Hospital
43. Lasso, Andras :: PerkLab, Queen's University
44. Lauer, Rebekka :: Humboldt University Berlin
45. Lisle, Curtis :: KnowledgeVis, LLC
46. Mastrogiacomo, Katie :: Brigham and Women's Hospital
47. Mateus, D. :: TUM
48. Mehrtash, Alireza :: Brigham and Women's Hospital
49. Meine, Hans :: University of Bremen
50. Meyer, Anneke :: University of Magdeburg
51. Miller, James :: GE Research
52. Mirabel, Clement :: University of Michigan
53. Nitsch, Jennifer :: University of Bremen
54. Norton, Isaiah :: Brigham and Women's Hospital
55. O'Donnell, Lauren :: Brigham and Women's Hospital
56. Oram, Louise :: The Intervention Centre-Oslo University Hospital
57. Padhy, Smruti :: Massachusetts Institute of Technology
58. Paniagua, Beatriz :: Kitware, Inc.
59. Parmar, Chintan :: DFCI-Harvard Medical School
60. Peled, Sharon :: Brigham and Women's Hospital
61. Pieper, Steve :: Isomics, Inc.
62. Pinter, Csaba :: Queen's University
63. Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School
64. Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School
65. Rankin, Adam :: Robarts Research Institute
66. Rheault, Francois :: Université de Sherbrooke
67. Roethe, Anna :: Humboldt University / Charité University Hospital Berlin
68. Sharp, Gregory :: Massachusetts General Hospital
69. Sridharan, Patmaa :: University of Pennsylvania-CBICA
70. Szasz, Teodora :: University of Chicago
71. Unadkat, Prashin :: Brigham and Women's Hospital
72. Van Griethuysen , Joost :: Netherlands Cancer Institute
73. Vidyaratne, Lasitha :: Old Dominion University
74. Wang, Yaofei :: Brigham and Women's Hospital
75. Wang, Ziyang :: Brigham and Women's Hospital
76. Wei, Dawei :: Brigham and Women's Hospital
77. Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School
78. Xu, Wanxin :: Brigham and Women's Hospital
79. Yang, Yixin :: Brigham and Women's Hospital
80. Ye, Wu :: Brigham and Women's Hospital
81. Zaffino, Paolo :: Magna Graecia University of Catanzaro, Italy
82. Zeleznik, Roman :: DFCI
83. Zhang, Fan :: Brigham and Women's Hospital
84. Zhang, Miaomiao :: Massachusetts Institute of Technology
85. Zhang, Yuqian :: Brigham and Women's Hospital
86. Zhou, Haoyin :: Brigham and Women's Hospital
87. Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital