2010 Summer Project Week

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Summary: The 11th PROJECT WEEK was held June 21-25, 2010 in Boston, at MIT and Brigham and Women's Hospital. It recorded 126 registered attendees, who worked on 71 projects. These attendees represented 30 academic sites and 15 companies. Participants traveled to the project week from 9 countries (Austria, Singapore, France, Germany, Japan, Italy, England, Poland, and Canada), and from 16 states within the US(MA, NY, NC, MD, CA, UT, OH, MO, GA, PA, CO, IA, FL, DC, CT, NM). The projects, agenda, and affiliations of attendees are detailed below.

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Contents

Projects

Segmentation

  1. Robust Statistics Segmenter Slicer Module (Yi Gao, Allen Tannenbaum, Ron Kikinis)
  2. Multi-scale Shape Based Segmentation for the Hippocampus (Yi Gao, Allen Tannenbaum)
  3. Prostate Segmentation from MRI (Andriy Fedorov, Yi Gao)
  4. Segmentation on Mesh Surfaces Using Geometric Information (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
  5. SPECTRE: Skull Stripping integration with Slicer (Nicole Aucoin, Min Chen)
  6. White Matter Lesion segmentation (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
  7. EMSegmentation: Automatic Intensity Initialization using KMeans (Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)
  8. LV scar segmentation display and fusion (Dana C. Peters, Felix Liu, BIDMC, Boston)
  9. The Vascular Modeling Toolkit in 3D Slicer (Daniel Haehn, Luca Antiga, Kilian Pohl, Johannes Schick, Steve Pieper, Ron Kikinis)

Registration

  1. The 3DSlicer Registration Case Library (Dominik Meier)
  2. Evaluation of Registration in Slicer (James Fishbaugh, Guido Gerig, Domink Meier)
  3. HAMMER: Deformable Registration (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
  4. Best Regularization Term for Demons Registration Algorithm (Rui Li, Greg Sharp)
  5. Fiducial-based deformable image registration (Nadya Shusharina, Greg Sharp)
  6. MR to Ultrasound Registration Methodology (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward, Andriy Fedorov)
  7. Groupwise Registration (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

Shape Analysis

  1. Shape Test Bench (Marc Niethammer, Sylvain Bouix)
  2. Median Shape by Boundary-based Distance (Tammy Riklin Raviv, Sylvain Bouix)
  3. Shape Analysis projects, integration with Slicer3 (Beatriz Paniagua, Martin Styner)
  4. Particle Based Shape Regression (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
  5. Automatic SPHARM Shape Analysis in 3D Slicer (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

Diffusion

  1. NAMIC Tools Suite for DTI analysis (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
  2. Implementing Two-tensor tractography in Slicer (Python) (Stefan Leinhard, James Malcolm, Demian Wasserman, C-F Westin, Yogesh Rathi)
  3. Efficient Diffusion Connectivity via Multi­directional F­star (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
  4. Fluid Mechanics Based Tractography (Nathan Hageman)
  5. QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data (Sudhir Pathak)

IGT

  1. MR to CT Registration for Prostate Brachytherapy Dose Calculation (Andriy Fedorov, Dominik Meier, Hans Johnson)
  2. Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound (Jason White, Steve Pieper, Junichi Tokuda, Pratik Patel?)
  3. Prostate Intervention(Junichi Tokuda, Tamas Ungi, Haiying Liu, Sam Song)
  4. Liver Ablation (Haiying Liu, Noby Hata)
  5. BrainLab-Aurora Hybrid Navigation (Isaiah Norton, Dan Marcus, Noby Hata)
  6. PerkStation Module (Tamas Ungi, Xiaodong Tao)
  7. Co-registration of PET and DWI Images for the targeting of Glioma Biopsies (Gareth Smith, Dominik Meir, Vince Magnotta)
  8. Implementing Open IGT Link to Virtual Place for research support (Nicholas Herlambang, Masakatsu Hoashi, Junichi Tokuda, Noby Hata)
  9. Tracking Neuroendoscope Using EM Tracker and OpenIGTLink (Laurent Chauvin, Junichi Tokuda, Noby Hata)
  10. Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery (Atsushi Yamada, Junichi Tokuda, Noby Hata)

Radiotherapy

  1. Dicom RT plugin (Greg Sharp, Tamas Ungi)
  2. Adaptive Radiation Therapy for H&N cancer (Marta Peroni,Polina Golland,Greg Sharp)
  3. Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

Analysis

  1. IA-FEMesh Slicer3 Finite Meshing Module (N Grosland, V Magnotta, C Lisle, S Pieper)
  2. Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
  3. Mouse brain cortical thickness analysis (Joohwi Lee, Ipek Oguz, Martin Styner)
  4. Primate image analysis using the standard Slicer pipeline (Yundi Shi, Martin Styner, Clement Vache, Mar Sanchez, Andriy Fedorov)
  5. MRSI module and SIVIC interface (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
  6. Femoral Fracture Classification Brainstorming Session (Karl Fritscher, Vince Magnotta, Peter Karasev, Curt Lisle, Ron Kikinis)
  7. Computer_Aided_Photodynamic_Therapy (E Pietka, D Spinczyk, P Szabelak)
  8. Quantification of Lesion Diffusion Disruption(M Scully, H J Bockholt)
  9. Lupus Lesion Segmentation and Review Statistics(M Scully, H J Bockholt)

Microscopy Image Analysis

  1. DICOM supplement 145  : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
  2. Microscopy Extensions for ITK : convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
  3. Import/Export Farsight-GoFigure results (Arnaud Gelas, Lydie Souhait, Kedar Grama, Raghav Padmanabhan, Sean Megason, Badri Roysam)
  4. JPEG2000 and HDF5 Image Readers in ITK (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
  5. ITK Spherical Harmonics filter for shape analysis of cell nuclei (Shantanu Singh, Kishore Mosaliganti, Arnaud Gelas, Sean Megason, Raghu Machiraju)
  6. ITK Analysis of Large Histology Datasets (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
  7. CTK Transfer function widget (Nicolas Rannou, Julien Finet, Arnaud Gelas, Stever Pieper)
  8. Seedings results comparison (Antonin Perrot-Audet, Raghav Padmanabhan, Kishore Mosaliganti, Badri Roysam, Sean Megason)
  9. ITK Multiphase and GPAC level sets (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
  10. Median binary pattern texture measures for cell nuclei segmentation (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
  11. Standards and Interfaces for Microscopy Image Analysis in ITK (whoever has an opinion, Sean Megason)

NA-MIC Kit Internals

  1. Module Inventory (Steve, Jim)
  2. Viewer Manager Factory (Alex Yarmarkovich, Kilian, Steve, Nicole)
  3. Programmatic use of Volume Rendering module (Andriy Fedorov, Yanling Liu, Alex Yarmarkovich, Jim Barabas, Johannes Schick)
  4. Inventory of Volume Rendering Functionality (Jim Barabas, Noby Hata)
  5. Consistent visual language for Slicer4: icon rework marathon (Wendy Plesniak)
  6. Slicer Wizard for PET/CT workflow (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)
  7. PythonQt and console widget (Steve Pieper, Jean-Christophe Fillion-Robin)
  8. VTKWidgets (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
  9. Superbuild (David Partyka, Steve Pieper, Katie Hayes)
  10. Paraview Support for Computational Anatomy (Michel Audette, Mike Bowers)
  11. Real-Time Volume Rendering for Virtual Colonoscopy (Hiro Yoshida, Yin Wu, Steve Pieper, Ron Kikinis)

Workflows and Integration

  1. Workflows and Service Oriented Architecture Solutions for Slicer3 Modules (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)

Agenda

Time Monday, June 21 Tuesday, June 22 Wednesday, June 23 Thursday, June 24 Friday, June 25
Project Presentations NA-MIC Update Day IGT Day Reporting Day
8:30am Breakfast Breakfast Breakfast Breakfast
9am-12pm 9am: NA-MIC Kit Update (Jim Miller)

Grier Rooms
----------------------------------------
9:20am: 3D Slicer Update (Steve Pieper)
Grier Rooms
----------------------------------------
10am: Superbuild Demo (Dave Partyka)
Grier Rooms
----------------------------------------
10:15am: Break
Grier Rooms
----------------------------------------
10:30-11am: OpenIGTLink Update (Junichi Tokuda)
Grier Rooms
----------------------------------------
11am-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
Star Room

9am-12pm: Breakout Session:
ITK (Luis Ibanez)


Star Room

9am-5pm: Breakout Session:
OpenIGTLink


Grier Rooms

10am-12pm: Project Progress Updates


Grier Rooms

12pm-1pm Lunch Lunch Lunch Lunch Lunch boxes; Adjourn by 1:30pm
1pm-5:30pm 1-1:05pm: Ron Kikinis: Welcome

Grier Rooms
----------------------------------------
1:05-3:30pm: Project Introductions (all Project Leads)
Grier Rooms
----------------------------------------
3:30-5:30pm: Tutorial: Getting Started with Qt (Adam Weinrich, Nokia)
32-155 (Stata Lecture Hall)

1-3pm: Breakout Session:
QT/Slicer (Steve, JC, J2)


Star Room
----------------------------------------
3-4pm: Tutorial Contest Presentations
Grier Rooms
----------------------------------------
4-5pm: Breakout Session:
Data Management (Stephen Aylward)
Star Room

12:45-1pm: Tutorial Contest Winner Announcement


Grier Rooms
----------------------------------------
1-3pm: Breakout Session:
Microscopy Image Analysis (Sean Megason)
Kiva Room
----------------------------------------
3-5pm: Breakout Session:
QA Training (Luis Ibanez)
Star Room
----------------------------------------
3-4pm: Breakout Session:
VTK Widgets (Nicole, Kilian, JC)
32-261 Room
----------------------------------------

5pm: Reception

R&D Pub

1-2pm: Breakout Session:
GWE (Marco Ruiz)


----------------------------------------
2-3pm: Simple Git (Steve Pieper) (Slides)
----------------------------------------
3-4pm: Breakout Session:
Volume Rendering Demos and Discussion (Yin Wu, Steve Pieper)

5:30pm Adjourn for the day Adjourn for the day Adjourn for the day Adjourn for the day

Please note:

Background

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the NA-MIC Kit, algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of NA-MIC, NCIGT, NAC, Harvard Catalyst, and CIMIT. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available here.

Logistics

  • Dates: June 21-25, 2010
  • Location: MIT. Grier Rooms A & B: 34-401A & 34-401B.
  • REGISTRATION: Please click here to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
  • Registration Fee: $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
  • Hotel: We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) Please click here to reserve. You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.
   All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of
   $189/night/room (plus tax).
   This rate is good only through June 1.

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

  • Here is some information about several other Boston area hotels that are convenient to NA-MIC events: Boston_Hotels. Summer is tourist season in Boston, so please book your rooms early.
  • For hosting projects, we are planning to make use of the NITRC resources. See Information about NITRC Collaboration


Preparation

  1. Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
  2. The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
  3. By 3pm ET on June 10, 2009: Complete a templated wiki page for your project. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
  4. By 3pm on June 17, 2010: Create a directory for each project on the NAMIC Sandbox (Zack)
    1. Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
    2. Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
    3. Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
  5. Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
  6. People doing Slicer related projects should come to project week with slicer built on your laptop.
    1. Projects to develop extension modules should work with the Slicer-3-6 branch (new code should not be checked into the branch).
    2. Projects to modify core behavior of slicer should be done on the trunk.

Attendee List

NOTE: THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD NOT EDIT THIS, BUT REGISTER BY CLICKING HERE.

  1. Yousef Al-Kofahi, CompuCyte Corporation
  2. Peter Anderson, retired
  3. Nicole Aucoin, Brigham & Women's Hospital
  4. Michel Audette, Kitware, Inc.
  5. Stephen Aylward, Kitware, Inc.
  6. Jim Barabas, MIT
  7. Barrett, Ryan, Brigham & Women's Hospital
  8. Alexis Boucharin, UNC Neuro Image Research and Analysis Laboratories
  9. Sylvain Bouix, Brigham & Women's Hospital
  10. Michael Bowers, Johns Hopkins University
  11. Francois Budin, UNC
  12. Everette Burdette, Acoustic MedSystems, Inc.
  13. Laurent CHAUVIN, Brigham and Women's Hospital
  14. Min Chen, Johns Hopkins University
  15. Jason Crane, UCSF
  16. Nikos Chrisochoides, College of William and Mary
  17. Manasi Datar, SCI Institute
  18. Liya Ding, The Ohio State University
  19. Ryan Eckbo, Brigham and Women's Hospital
  20. Ilker Ersoy, University of Missouri Columbia
  21. Andriy Fedorov, Surgical Planning Lab
  22. Jean-Christophe Fillion-Robin , Kitware, Inc.
  23. Julien Finet, Kitware, Inc.
  24. James Fishbaugh, SCI Institute
  25. Karl Fritscher, UMIT
  26. Yi Gao, Gerogia Tech
  27. Arnaud GELAS, Harvard Medical School
  28. Randy Gollub, MGH
  29. Chris Gorgolewski, Surgical Planning Laboratory
  30. alexandre gouaillard, CoSMo Software
  31. Sylvain Gouttard, SCI Institute
  32. Kedar Grama, Rensselaer Polytechnic Institute
  33. Daniel Haehn, University of Pennsylvania
  34. Adel Hafiane, ENSI-Bourges
  35. Nathan Hageman,
  36. Dieter Hahn, University Erlangen
  37. Michael Halle, Surgical Planning Laboratory, Brigham & Women's Hospital
  38. Corentin Hamel, UNC Chapel Hill
  39. Nobuhiko Hata, Brigham and Women's Hospital
  40. Kathryn Hayes, Brigham and Women's Hospital
  41. Nicholas Herlambang, AZE, Ltd.
  42. Masakatsu Hoashi, AZE Ltd.
  43. Leslie Holton, Medtronic Navigation
  44. Luis Ibanez, Kitware, Inc.
  45. Jayender Jagadeesan, Surgical Planning Laboratory, Brigham & Women's Hospital
  46. Hans Johnson, University of Iowa
  47. Tina Kapur , Brigham and Women's Hospital
  48. Peter Karasev, Georgia Tech
  49. Ron Kikinis, Brigham and Women's Hospital
  50. Minjeong Kim, UNC-Chapel Hill
  51. Ivan Kolesov, Georgia Institute of Technology
  52. Garrett Larson, UNC-CH
  53. Joohwi Lee, UNC Chapel Hill
  54. Rui Li, MGH
  55. Stefan Lienhard, LMI
  56. Curtis Lisle, KnowledgeVis, LLC
  57. Haiying Liu, Brigham and Women's Hospital
  58. Felix Liu, Beth Israel Deaconess Medical Center
  59. Yanling Liu, SAIC-Frederick, Inc.
  60. Bradley Lowekamp, Lockheed Martin
  61. raghu machiraju, The Ohio State University
  62. Vincent Magnotta, The University of Iowa
  63. mathieu malaterre, CoSMo Software
  64. Charles Maneval, Brigham & Women's Hospital
  65. Daniel Marcus, Washington University
  66. William Marks, Focused Ultrasound Lab, Brigham & Women's Hospital, Harvard Medical School
  67. Katie Mastrogiacomo, Brigham and Women's Hospital
  68. Joy Matsui, University of Iowa
  69. Sean Megason, Harvard Medical School
  70. Dominik Meier, Brigham & Women's Hospital
  71. Bjoern Menze, CSAIL MIT
  72. Mikhail Milchenko, WUSTL
  73. James Miller, GE Research
  74. Kishore Mosaliganti, Harvard Medical School
  75. Marc Niethammer, UNC Chapel Hill
  76. Isaiah Norton, Brigham & Women's Hospital, Neurosurgery
  77. Beck Olson , UCSF
  78. John Onofrey, Yale University
  79. Raghav Padmanabhan, RPI
  80. Kannappan Palaniappan , University of Missouri
  81. Beatriz Paniagua, University of North Caolina at Chapel Hill
  82. Xenophon Papademetris, Yale University
  83. Eun-Joo Park, Brigham & Women's Hospital
  84. David Partyka, Kitware, Inc.
  85. Pratik Patel,
  86. Sudhir Pathak, Univeristy Of Pittsburgh
  87. Thierry PECOT, Ohio State University
  88. Marta Peroni, Politecnico di Milano
  89. Antonin Perrot-Audet , Harvard Medical School
  90. Steve Pieper, Isomics, Inc.
  91. Wendy Plesniak, Brigham and Women's Hospital
  92. Kilian Pohl, IBM
  93. Sonia Pujol, Brigham and Women's Hospital
  94. Nicolas Rannou, Harvard Medical School
  95. Tammy Riklin Raviv, MIT, CSAIL
  96. Marco Ruiz, UCSD
  97. Johannes Schick, Surgical Planning Laboratory
  98. William Schroeder, Kitware, Inc.
  99. Mark Scully, The Mind Research Network
  100. Gunasekaran Seetharaman, US Air Force Research Lab
  101. Greg Sharp, MGH
  102. Yundi Shi, UNC Chapel Hill
  103. Nadya Shusharina, MGH
  104. Shantanu Singh , The Ohio State University
  105. Gareth Smith , Wolfson Medical Imaging Centre (WMIC)
  106. Lydie Souhait, Harvard Medical School
  107. Dominik Spinczyk, Silesian University of Technology
  108. Padmapriya Srinivasan,
  109. Xiaodong Tao, GE Research
  110. Matthew Toews , Brigham and Women's Hospital, Harvard Medical School
  111. Junichi Tokuda, Brigham and Women's Hospital
  112. Tamas Ungi, Queen's University
  113. Clement Vachet, UNC Chapel Hill
  114. Veda Vadyar, Brigham and Women's Hospital
  115. Gopalkrishna Veni, SCI Institute
  116. Stuart Wallace, Massachusetts General Hospital
  117. Demian Wassermann, Surgical Planning Laboratory, LMI, PNL
  118. Yihan Wei, Brigham and Women's Hospital
  119. Adam Weinrich, Nokia
  120. Sandy Wells, Brigham and Women's Hospital
  121. Phillip White, Brigham and Women's Hospital, Harvard Medical School
  122. Guorong Wu, University of North Carolina at Chapel Hill
  123. Yin Wu, Mass General Hospital
  124. Atsushi Yamada, Nagoya Institute of Technology
  125. Alexander Yarmarkovich, ISOMICS
  126. Alexander Zaitsev, Brigham and Womens Hospital
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