2017 Winter Project Week

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Welcome to the web page for the 24th Project Week!

Summary

The 24th NA-MIC Project Week open source hackathon was held during the week of January 9-13, 2017 at MIT. It recorded 99 registered attendees, who worked on 55 projects.

A summary of all past Project Events.

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.

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

Deep Learning and GPUs

1. Deep Learning for Medical Image Computing (Tina Kapur)
2. Needle Segmentation from MRI (Paolo Zaffino, Ziyang Wang, Guillaume Pernelle, Tina Kapur)
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, Charles Guttmann)
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. Population Based Image Imputation (Adrian Dalca, Katie Bouman, Mert Sabuncu, Polina Golland)
9. Knee Cartilage Segmentation (Hans Meine)

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, Satra Ghosh)
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)
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, 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, David Garcia, Julian Smith, Warren Rozen, David Hunter-Smith)
6. Visualization Concept for Intraoperative Use of Functional Mapping Data (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)
7. Integrative Interface for Intraoperative Software Applications (Anna Roethe, Rebekka Lauer, 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. WMA & 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, Johan Andruejol, JC Fillon-Robin, James Fishbaugh, Priscille de Dumast)
2. Mandibular and maxillary Shape Regression (Beatriz Paniagua, Clement Mirabel, Priscille de Dumast, James Fishbaugh, Lucia Cevidanes, Daniella Garib)
3. Slicer + VR = <3 (Adam Rankin, Andras Lasso, Ryan D'Souza (NDI), Matthew Jolley (Children's Hospital of Philadelphia), Kitware+Slicer dev (JC,JFinet,etc...)
4. Slicer for Hyperspectral Ophthalmology Analysis (Sungmin Hong)
5. Geodesic Segmentation and Lung tumor Analysis (Patmaa S,)
6. Prostate Gland Sector Segmentation (Anneke Meyer, Andrey Fedorov, Alireza Mehrtash, Christian Hansen, Teodora Szasz)
7. Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery (Jennifer Nitsch, Hans Meine)
8. Segmentation of meningiomas in structural MR images (Jakub Kaczmarzyk, 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. Improvements to Segment Editor (Csaba Pinter, Andras Lasso)
3. Plastimatch multi-planar and multi-metric registration (Greg Sharp)
4. Updating Slicer Community Infrastructure (Discourse, GitHub, Gitter, ???) (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)
5. Slicer support for interactive modification of 3D models (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
6. Support for volumetric meshes (Alexis Girault, Curtis Lisle, Steve Pieper)
7. Improve Matlab integration (Alexis Girault)
8. Slicer* Community Topics, Projects, Flavors: The SLICERVERSE (Beatriz Paniagua, Lauren O'Donnell, Isaiah Norton, Gregory Sharp, Louise Oram)

Training and Dissemination

1. Tutorial contest (Sonia Pujol)
2. NVIDIA Demo Contest (Abdul Halabi, Abel Brown)
3. Project Week Survey (Krisztina Fischer, Tina Kapur)
4. Next project week: PW#25 (Paolo Zaffino, Maria Francesca Spadea, Tina Kapur)

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