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. Deep Learning for Medical Image Computing (Tina Kapur)
2. Needle Segmentation from MRI (Tina Kapur, Ziyang Wang, Guillaume Pernelle, Paolo Zaffino)
3. DeepInfer: Open-source Deep Learning Deployment Toolkit (Alireza Mehrtash, Mehran Pesteie, Yang (Silvia) Yixin, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)
4. Diffusely abnormal white matter segmentation with 3d U-net (Mohsen Ghafoorrian, Bram Platel, Sandy Wells, Tina Kapur)
5. Deep Learning for Synthetic MRI (Frank Preiswerk, Yaofei "Ada" Wang)
6. An open-source tool to classify TMJ OA condyles (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)
7. Evaluate Deep Learning for binary cancer lesion classification (Curt Lisle)
8. Convolutional neural nets for lung cancer survival prediction (Ahmed Hosny, Chintan Parmar, Roman Zeleznik, Hugo Aerts)
9. Population Based Image Imputation (Adrian Dalca, Katie Bouman, Polina Golland)

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. IPFS and NoSQL for cloud databases (Hans Meine, Steve Pieper)
4. Explore integration of Web-based imaging workflows with Slicer (Curt Lisle, Satra Gosh, Steve Peiper)
5. Web-based system to federate biological, clinical and morphological data (Juan Carlos Prieto, Clément Mirabel)
6. OAuth2.0 authentication in SlicerPathology (Erich Bremer, Steve Pieper, Teodora Szasz)
7. Electron App to add, navigate and visualize DICOM images (Smruti Padhy, Satrajit Ghosh, Mathias Goncalves)
8. AMI: A 3D Medical Imaging Javascript Library (Rudolph Pienaar, Jorge Luis Bernal Rusiel, Nicolas Rannou)
9. Medical Visualizer using ParaViewWeb (Teodora Szasz)

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. Liver resection planning extension (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
5. 3D surgical planning solution for autologous breast reconstruction (Michael Chae, Andras Lasso, Julian Smith, Warren Rozen, David Hunter-Smith)
6. Visualization Concept for Intraoperative Use of Functional Mapping Data (Rebekka Lauer, Anna Roethe, Prashin Unadkat, Sarah Frisken)

dMRI

1. Fiber endpoint analysis for neurosurgical planning (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 (Shun Gong, Ye Wu, Isaiah Norton, Fan Zhang, 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 (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
2. DICOM QuantitativeReporting (Christian Herz, Andrey Fedorov, Andras Lasso, Csaba Pinter)
3. PyRadiomics library (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christophe Fillion-Robin)
4. PkModeling - DCE Modeling Accuracy and UI/UX Update (Andrew Beers)
5. Manual Segmentation Module w/ Subtraction Maps + Delaunay Models (Andrew Beers)

Shape Analysis, Segmentation

1. Slicer for Shape Analysis (Beatriz Paniagua)
2. Mandibular Shape Regression (Beatriz Paniagua, James Fishbaugh)
3. Slicer & HoloLens (Adam Rankin, Andras Lasso)
4. Slicer for Hyperspectral Ophthalmology Analysis (Sungmin Hong)
5. Geodesic Segmentation and Lung tumor Analysis (Patmaa S, Sarthak Pati, Ratheesh k, Mark B, Yong F, Despina K, Ragini V, Christos D)
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)

Infrastructure

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

Training and Dissemination

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