NA-MIC Project Weeks

Welcome to the web page for the 35th Project Week!

This event was held virtually June 28-July 2, 2021.

Numbers and Introduction

• 140 Registered Attendees. 44% First Timers!
• 23 countries.
  • Bimodal Time Zone Distribution (UTC-4 and UTC+1).
• 29 Projects.
• All sessions except for work in project teams will happen on Zoom. Please see google calendar entries for links for both zoom and discord.
• Begin with the good old recipe of in-person Project Weeks.
  • Each team delegates a member to present the project in a maximum of 90 seconds using the project page.
  • Hope your project page is ready and any image you want to show is up there. There will not be enough time to share your screen, we will simply share your project page on the zoom session.
• Presenters - please stick with the allocated time, if your internet connection has problems during your presentation, we will move to the next speaker and we can accommodate your talk at the, end time permitting.
• Audience - please ask the speaker questions using zoom chat or the discord server chat.
• Work in project teams will happen throughout the week.
  • A Discord server has been set up with a voice/video channel and a text channel for every project on the main webpage.
  • We will have a walkthrough of the discord server and project channels as the last project presentation today.
  • You can use the channels to coordinate the work of your team.
  • It is recommended to hold a first meeting of the team on the voice channel of the project after project presentations on Monday.
  • Please do everything you can to accommodate all team members in terms of schedule, especially the ones with family constraints living in time zones that are less favored by the schedule of Project Week.
• The program includes optional introductory lectures (8-9:30 Tue-Wed-Thu) and breakout sessions (10-12 Tue-Wed-Thu), all happening on Zoom.
  • Tuesday: AI-assisted annotations (lectures), What’s new in Slicer and a QnA session that was very popular last year
  • Wednesday: Image Guided Surgery lectures and breakout session on the same topic
  • Thursday: Web-based tools lecture, and breakout session on Human Brain Atlases
• We will end the week with project results presentation. A member from each team will present their results in a maximum of 90 seconds minutes using project page as a visual support for the presentation, so please make sure it is up to date with your latest results by Friday morning.

Attendees

• Step 0: REGISTER here
• Step 1: Sign-up on the discourse forum to get updates and ask questions.
• Step 2 (optional): Join the Discord server to help prepare and work on your project: Invite Link

Agenda

How to add this calendar to your own?

Breakout sessions complementary material

• What’s new in Slicer(Andras Lasso, Jean-Christophe Fillion-Robin, Sam Horvath, Steve Pieper)
• MONAI introductory presentation (Wenqi Li, NVIDIA)
• MONAI Label introductory presentation (Andres Diaz-Pinto, King’s College London)
• DICOM Overview (Steve Pieper)
• OHIF v3 and a glance into Cornerstone 3D (Erik Ziegler, Alireza Sedghi)
• NCI Imaging Data Commons (Andrey Fedorov)

Projects (How to add a new project?)

VR/AR and Rendering

1. PRISM volume rendering (Simon Drouin, Steve Pieper, Kyle Sunderland, Andrey Titov, Rafael Palomar)
2. SlicerVR build and in-VR widgets (Csaba Pinter, Adam Rankin, Jean-Christophe Fillion-Robin)
3. Virtual cameras (Étienne Léger, Tamas Ungi, Andras Lasso)
4. TMS Visualization in Slicer (Loraine Franke, Lipeng Ning, Yogesh Rathi, Steve Pieper, Raymond Yang, Daniel Haehn)
5. AR in Slicer (Alicia Pose Díez de la Lastra, Javier Pascau, Csaba Pinter)
6. Interactive Slice Intersections (David García-Mato, Kyle Sunderland, Csaba Pinter)
7. VR for Birth Delivery Training (Mónica García-Sevilla, David García-Mato, Abián Hernández-Guedes, Juan Ruiz Alzola, Javier Pascau, Nayra Pumar, Csaba Pinter)
8. VR display plugin for PyDBS using a zSpace device (Marine Camba, Sara Fernandez Vidal, Sinan Haliyo)

IGT

1. NousNav (Alexandra Golby, Sam Horvath, Sarah Frisken, David Allemang, Tina Kapur, Steve Pieper, Jean-Christophe Fillion-Robin, Sonia Pujol)
2. DBS Navigation (Simon Oxenford)
3. Slicer module for planning MR-guided focal cryoablation of prostate cancer (Pedro Moreira)
4. Slicer-Liver: planning liver resections in 3D Slicer (Rafael Palomar, Gabriella d’Albenzio, Ole Vegard Solberg, Geir Arne Tangen)
5. ROS2 - 3D Slicer Integration (Junichi Tokuda, Tamas Ungi, Axel Krieger, Simon Leonard, Mark Fuge)
6. IGT training material for francophone countries (Nayra Pumar, Mohamed El Moctar Septy, Yahya Tfeil, Asmaa Skareb, Marilola Afonso, Juan Ruiz Alzola)
7. GPU Rigid Registration (Gelel Rezig, Houssem Eddine Gueziri, Simon Drouin)
8. Planar Osteotomies Virtual Surgical Planning And Patient-Specific Surgical Guides (Mauro I. Dominguez, Manjula Herath)
9. Marklerless Tracking for Low-Cost neuronavigation for TMS (Julie Alvarez (Neurotrauma Center), Gabriel Vargas Grau (Universidad de Santander), Juan Camilo Gamboa (Mc Gill University), Andrés Gamboa (Neurotrauma/Universidad Politécnica de Valencia/))
10. IGT Equipment for ReUse (Tina Kapur, Gabor Fichtinger, +)
11. OpenIGTLink (Junichi Tokuda)
12. US-CT Vertebra Registration (Houssem Gueziri, Tamas Ungi)

Deep learning and segmentation

1. DeepHeart MONAILabel integration (Matthew Jolley, Christian Herz, Danielle F. Pace, Andras Lasso)
2. Registration for Deep Learning (Curtis Lisle, Neha Goyal, Greg Sharp)
3. Integration of PyTorch and Slicer (Fernando Pérez-García, Andrés Díaz-Pinto, Andras Lasso, Curtis Lisle, Rebecca Hisey, Steve Pieper, Tamas Ungi)
4. Development of Deep Learning Segmentation for Spines with Metastatic Disease (Ron Alkalay, Curtis Lisle, Andres Diaz-Pinto)
5. Development of Deep Learning Based Brain Masking (Raymond Yang, Lipeng Ning, Yogesh Rathi, Steve Pieper, Loraine Franke, Daniel Haehn)
6. Deep Learning for Subcortical Brain Segmentation (Jarrett Rushmore, Elizabeth Kenneally, Sylvain Bouix, Kyle Sunderland, Nikos Makris)
7. Time-Series Segmentation Module(Rebecca Hisey, Tamas Ungi, Andras Lasso, Andres Diaz-Pinto, Tina Kapur)
8. MONAI Label(Andres Diaz-Pinto, Fernando Pérez-García, Sachidanand Alle, Alvin Ihsani, Vishwesh Nath)

Cloud, open data and annotation

1. SlicerOnDemand (Steve Pieper, Curt Lisle, Andrey Fedorov, Theodore Aptekarev)
2. NCI Imaging Data Commons (Andrey Fedorov, Markus Herrmann, Theodore Aptekarev, Steve Pieper, Ron Kikinis)
3. mpReview: Development of a streamlined Slicer module for (manual) image annotation (Andrey Fedorov, Dora Szasz, Masoom Haider, Aytek Oto, Andras Lasso, Fiona Fennessy)
4. DICOM-SR: Extending DICOM-SR support in dcmjs and adding test cases (Emel Alkim, Steve Pieper, Andrey Fedorov)
5. Slicer for Microscopy Data (Sindhura Thirumal, Steve Pieper, Tina Kapur)
6. Discourse Meet and Greet(Simon Drouin)

Registrants

Do not add your name to this list below. It is maintained by the organizers based on your registration. Register here.

List of registered participants so far (names will be added here after processing registrations):

1. Mónica García Sevilla , Universidad de Las Palmas de Gran Canaria , Gran Canaria , Spain
2. ZhenXiao Yu , University Of Western Ontario , Ontario , Canada
3. Shreyas Chandra Sekhar , WPI , CA , USA
4. Tina Kapur , Brigham and Women’s Hospital and Harvard Medical School , MA , United States
5. Sam Horvath , Kitware , North Carolina , United States
6. Steve Pieper , Isomics, Inc. , MA , US
7. Simon Oxenford , Charite Berlin , Berlin , Germany
8. Theodore Aptekarev , None , Moscow/Tel Aviv , Israel/Russia
9. Samuelle St-Onge , École de Technologie Supérieure , Montreal , Canada
10. Csaba Pinter , Ebatinca / Pixel Medical , Canarias , Spain
11. Miguel Xochicale , King’s College London , London , UK
12. Thibault Pelletier , Kitware , Rhône-Alpes , France
13. Saima Safdar , UWA , Western australia , Australia
14. Juan Ruiz-Alzola , University of Las Palmas de Gran Canaria , Canarias , Spain
15. David García Mato , Ebatinca S.L. , Las Palmas , Spain
16. Mario Banfoldy , Banfoldy and Partners , SP , Brasilien
17. Simon Drouin , École de Technologie Supérieure , Montreal , Canada
18. Ron Kikinis , Harvard Medical School , Boston , United States
19. Herbert Shin , University of Western Ontario , , Canada
20. Ahmedou Moulaye IDRISS , Faculty of Medicine / University of Nouakchott Al Aasriya , Nashville , Mauritania
21. Ron Alkalay , Beth Israel Deaconess Medical Center , Bosotn , US
22. Alicia Pose Díez de la Lastra , Universidad Carlos III de Madrid , Leganés , España
23. Chenglin Zhu , Cornell University , Ithaca , Study in US, live in China
24. Jarrett Rushmore , BU/BWH/MGH , Boston , USA
25. Walia Farzana , Old Dominion University , Norfolk , United States of America
26. Mamadou Samba Camara , University Cheikh Anta Diop of Dakar , Dakar , Senegal
27. Fernando Pérez-García , UCL & King’s College London , , United Kingdom
28. Curtis Lisle , KnowledgeVis, LLC , Altamonte Springs , United States
29. Tamas Ungi , Queen’s University , Kingston , Canada
30. Andras Lasso , PerkLab, Queen’s University , Kingston , Canada
31. Junichi Tokuda , Brigham and Women’s Hospital , Boston , United States
32. Maximilian Fischer , German Cancer Research Center , , Germany
33. Marilola Afonso , Universidad de Las Palmas de Gran Canaria , Las Palmas de Gran Canaria , Spain
34. Étienne Léger , Concordia University , Montréal , Canada
35. Idafen Santana-Perez , University of Las Palmas de Gran Canaria , Las Palmas de Gran Canaria , Spain
36. Loraine Franke , University of Massachusetts Boston , Boston , United States
37. Varun Kumar Agarwal , Bareilly International University , Bareilly , India
38. Christian Herz , Children’s Hospital of Philadelphia , , United States
39. Mohamed El Moctar SEPTY , Medical School of Nouakchott- UNA , Nouakchott , Mauritania
40. TFeil Yahya , Faculty of Medicine of University of Nouakchott Al Aasriya , Nouakchott , Mauritania
41. Joshua Bierbrier , McGill University , Montreal , Canada
42. Leah Groves , Western University , London , Canada
43. Alfredo Morales Pinzon , BWH , Boston , United States
44. Sylvain Bouix , BWH , Boston , USA
45. Ahmedou Moulaye IDRISS , Faculty of Medicine - University Nouakchott Al Aasriya , Nouakchott , Mauritania
46. Sonia Pujol , Brigham and Women’s Hospital, Harvard Medical School , Boston , USA
47. Raymond Yang , University of Massachusetts Boston , Edison , United States of America
48. Sarah Frisken , Brigham and Women’s Hospital , Boston , USA
49. Pedro Moreira , Brigham and Women’s Hospital , Boston , USA
50. Rebecca Hisey , Queen’s University , Kingston , Canada
51. Andrey Titov , École de technologie supérieure , Saint-Bruno-de-Montarville , Canada
52. Li Zhenzhu , HuaMei Hospital, University of Chinese Academy of Sciences , NingBo , China
53. Ed Yeterian , Colby College , Pineville , USA
54. Renzo Phellan Aro , McGill University , Montreal , Canada
55. Fahd Derkaoui Hassani , Cheikh Zaid international University Hospital / UIASS , Rabat , Morocco
56. Elizabeth Kenneally , Tufts University , Somerville , United States
57. Lidia Al-Zogbi , Johns Hopkins University , Baltimore , United States
58. Andrey Fedorov , Brigham and Women’s Hospital , Cambridge , United States
59. Jayender Jagadeesan , Brigham and Women’s Hospital , Boston , US
60. Gelel Rezig , Ecole de Technologie Supérieure , Montréal , Canada
61. Souleymane Diao , Cheikh Anta Diop University , Dakar , Sénégal
62. Rafael Palomar , Oslo University Hospital / NTNU , Oslo , Norway
63. Gabriella d’ Albenzio , Oslo University Hospital , Oslo , Norway
64. Ole Vegard Solberg , SINTEF , Trondheim , Norway
65. Mauro I. Dominguez , M3Dical , Hughes , Argentina
66. Adam Rankin , Robarts Research Institute , London , Canada
67. Javier Pascau , Universidad Carlos III de Madrid , Madrid , Spain
68. Yoga Balagurunathan , Moffitt Cancer Center , Tampa , USA
69. Zhouping Wei , Moffitt Cancer Center , Tampa , US
70. Abián Hernández , Universidad de Las Palmas de Gran Canaria (ULPGC) , Las Palmas de Gran Canaria , Spain
71. Andinet Enquobahrie , Kitware , CARY , United States
72. Andrés Gamboa , Neurotrauma Center/Universidad Politécnica de Valencia , Bucaramanga/Valencia , Colombia/España
73. Marine CAMBA , CENIR, Paris Brain Institute , Paris , France
74. Teodora Szasz , The University of Chicago , Chicago , United States
75. Geir Arne Tangen , SINTEF , Trondheim , Norway
76. John Witt , Georgetown University, CHOP , Philadelphia , United States
77. Andres Diaz-Pinto , KCL , London , United Kingdom
78. Masoom Haider , University of Toronto , Toronto , Canada
79. Neha Goyal , University of Massachusetts Boston , Boston , United States
80. Batuhan Gundogdu , University of Chicago , Chicago , United States
81. Caio A Neves , University of Brasilia , Brasilia , Brazil
82. Laleh Seyyed-Kalantari , Mount Sinai health , Toronto , Canada
83. Nayra Pumar , EBATINCA , Las Palmas de Gran Canaria , Spain
84. Emel Alkim , Stanford University , MOUNTAIN VIEW , United States
85. Jean-Christophe Fillion-Robin , Kitware , Carrboro , USA
86. Lucas Gandel , Kitware , Villeurbanne , France
87. Sara Fernandez Vidal , ICM , Paris , France
88. Daniel Haehn , University of Massachusetts Boston , Boston , United States
89. Alberto Santamaria-Pang , Microsoft , Redmond , United States
90. Jameson Merkow , Microsoft , San Diego , USA
91. Risto Rangel , Microsoft , Redmond , United States
92. David Allemang , Kitware, Inc. , Carrboro , USA
93. Rudolf Bumm , Cantonal Hospital Graubünden, Department of Surgery , Chur , Switzerland
94. Gordon Harris , Massachusetts General Hospital , Boston , United States
95. Amber Wood-Bailey , University of Liverpool , Liverpool , United Kingdom
96. Lucia Cevidanes , University of Michigamn , Ann Arbor , United States
97. Ernest Namdar , University of Toronto , Toronto , Canada
98. Belkis Abufaur , The Cyprus Institute , , Turkey
99. Niral , Johns Hopkins University , Baltimore , USA
100. Rohan Vijayan , Johns Hopkins University , Baltimore , United States of America
101. Miguel Xochicale , King’s College London , London , United Kingdom
102. Nayra Pumar , Ebatinca , Las Palmas de Gran Canaria , Spain
103. Izabel Rubira-Bullen , Bauru Dental School - University Sao Paulo , Bauru - Sao Paulo , Brazil
104. Paolo Zaffino , Magna Graecia University of Catanzaro , Lamezia Terme , Italy
105. Nadya Shusharina , Massachusetts General Hospital , Boston , United States
106. Greg Sharp , Massachusetts General Hospital , Boston , USA
107. Nick Jowkar , Brigham and Women’s Hospital , Boston , USA
108. leo zekelman , Harvard Medical School , Boston , USA
109. Parikshit Juvekar , Brigham & Women’s Hospital , Boston , USA
110. Axel Krieger , Johns Hopkins University , Baltimore , United States
111. Abby Recko , Colby College , Waterville , USA
112. YuhJong Liu , University of Pennsylvania , Philadelphia , US
113. Houssem Gueziri , Montreal Neurological Institute , Montreal , Canada
114. Kyle Sunderland , Queen’s University , Kingston , Canada
115. Manjula Herath , Malmo University , Malmö , Sweden
116. Badiaa Ait Ahmed , Abdelmalek Essaâdi University , Tétouan , Morocco
117. Lipeng Ning , Brigham and Women’s Hospital , Boston , USA
118. Sindhura Thirumal , Queen’s University , Kingston , Canada
119. Swajan Paul , McGill University , Montreal , Canada
120. Jesse Thompson , University of Hawaii John A Burns School of Medicine , Honolulu , Hawaii
121. Michael Halle , Brigham and Women’s Hospital , Boston , MA
122. Chenglin Zhu , Cornell University , Ithaca , USA/China
123. Onder Erin , Johns Hopkins University , Baltimore , United States
124. Eberto Benjumea , Universidad Tecnológica de Bolívar , Cartagena , Colombia
125. Clare Tempany , BWH , Boston , USA
126. Nicholas Fordham , Boston University School of Medicine , Boston , United States
127. Dr. Gerard Rushingabigwi , University of Rwanda , , Rwanda
128. Joanna James , Beth Israel Deaconess Center , Boston , USA
129. Mick Ganza , University of Rwanda, CEBE , Kigali , Rwanda
130. Xiaolong Liu , Johns Hopkins University , Baltimore , United States
131. Mushimiyimana Sophie , University of Rwanda , , Rwanda
132. UWIZEYIMANA MEDIATRICE , UR/NYARUGENGE CAMPUS , KIGALI , RWANDA
133. Erik Ziegler , Radical Imaging / Open Health Imaging Foundation , , France
134. Alireza Sedghi , Radical Imaging / Open Health Imaging Foundation , Toronto , Canada
135. Laleh Seyyed-Kalantari , Sinai Health , Thornhill , Canada
136. FELIX HARERIMANA , UNIVERSITY OF RWANDA , RWAMAGAN , RWANDA
137. Xavier Riobé , Certis Therapeutics , Bordeaux , France
138. Lucas Ewing , Harvey Mudd College , Boston , US
139. Naghmeh Ansari , Concordia University , Montreal , Canada
140. Randy Gollub , MGH , Lexington , USA

History

Please read about our experience in running these events since 2005: Increasing the Impact of Medical Image Computing Using Community-Based Open-Access Hackathons: the NA-MIC and 3D Slicer Experience.

Logistics

• Dates: June 28-July 2, 2021.
• Location: THE INTERNET