2010 Summer Project Week

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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

Agenda

Monday, June 21, 2010

Tuesday, June 22, 2010

    • 8:30am breakfast
    • 9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
    • 9:45-10:30am 3D Slicer Update (Steve Pieper)
    • 10:30-11am OpenIGTLink Update (Junichi Tokuda)
    • 11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
    • noon lunch
    • 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
    • 3pm: Tutorial Contest Presentations
    • 4-5pm 2010 Summer Project Week Breakout Session: Data Management (Dan Marcus, Stephen Aylward)
    • 5:30pm adjourn for day

Wednesday, June 23, 2010

Thursday, June 24, 2010

    • 8:30am breakfast

Friday, June 25, 2010

Projects

Segmentation

Registration

IGT

Radiotherapy

Analysis

Microscopy Image Analysis

  • Malaterre, Gouaillard: DICOM supplement 145: Microscopy Image in the Dicom Standard
  • Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
  • Gouaillard: Flow Cytometry
  • Import/Export Farsight-GoFigure results (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
  • Arnaud Gelas, Sean Megason, Badri Roysam: Wrapping FARSIGHT nuclear segmentation algorithm as a GoFigure plugin.
  • ITK Spherical Harmonics filter for shape analysis of cell nuclei (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
  • CTK Transfer function widget (Nicolas Rannou, Julien Finet, Stever Pieper)
  • Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason, Badri Roysam: Seeding results comparison
  • ITK GPAC level set (K. Palaniappan, Kishore Mosaliganti, Sean Megason)

Shape Analysis

  • Median Shape by Boundary-based Distance (Tammy Riklin Raviv, Sylvain Bouix)

Informatics

  • Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

Diffusion

NA-MIC Kit Internals

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. Aucoin, Nicole, BWH
  2. Audette, Michel, Kitware
  3. Aylward, Stephen, Kitware, Inc
  4. Boucharin, Alexis, UNC Neuro Image Research and Analysis Laboratories
  5. Bouix, Sylvain, BWH
  6. Budin, Francois, UNC
  7. Burdette, Everette, Acoustic MedSystems, Inc.
  8. Chen, Min, Johns Hopkins University
  9. Datar, Manasi, SCI Institute
  10. Eckbo, Ryan, BWH
  11. Fedorov, Andriy, Surgical Planning Lab
  12. Fillion-Robin, Jean-Christophe, Kitware Inc.
  13. Finet, Julien, Kitware Inc
  14. Fishbaugh, James, SCI Institute
  15. Gao, Yi, Gerogia Tech
  16. GELAS, Arnaud, Harvard Medical School
  17. gouaillard, alexandre, CoSMo Software
  18. Gouttard, Sylvain, SCI Institute
  19. Haehn, Daniel, University of Pennsylvania
  20. Hageman, Nathan
  21. Hahn, Dieter, University Erlangen
  22. Hamel, Corentin, UNC Chapel Hill
  23. Hata, Nobuhiko, Brigham and Women's Hospital
  24. Hayes, Kathryn, Brigham and Women's Hospital
  25. Holton, Leslie, Medtronic Navigation
  26. Ibanez, Luis, KITWARE Inc.
  27. Johnson, Hans, University of Iowa
  28. Kapur, Tina, Brigham and Women's Hospital
  29. Kikinis, Ron, Brigham and Women's Hospital
  30. Kim, Minjeong, UNC-Chapel Hill
  31. Kolesov, Ivan, Georgia Institute of Technology
  32. Larson, Garrett, UNC-CH
  33. Li, Rui, MGH
  34. Lisle, Curtis, KnowledgeVis, LLC
  35. Liu, Haiying, Brigham and Women's Hospital
  36. Liu, Yanling, SAIC-Frederick, Inc.
  37. Magnotta, Vincent, The University of Iowa
  38. malaterre, mathieu, CoSMo Software
  39. Mastrogiacomo, Katie, Brigham and Women's Hospital
  40. Matsui, Joy, University
  41. Megason, Sean, Harvard Medical School
  42. Meier, Dominik, BWH, Boston MA
  43. menze, bjoern, CSAIL MIT
  44. Mosaliganti, Kishore, Harvard Medical School
  45. Niethammer, Marc, UNC Chapel Hill
  46. Norton, Isaiah, BWH Neurosurgery
  47. Paniagua, Beatriz, University of North Caolina at Chapel Hill
  48. Papademetris, Xenophon, Yale University
  49. Partyka, David, Kitware Inc
  50. Pathak, Sudhir, Univeristy Of Pittsburgh
  51. Peroni, Marta, Politecnico di Milano
  52. Perrot-Audet, Antonin, Harvard Medical School
  53. Pieper, Steve, Isomics, Inc.
  54. Plesniak, Wendy, BWH
  55. Pohl, Kilian, IBM
  56. Pujol, Sonia, Brigham and Women's Hospital
  57. Rannou, Nicolas, Harvard Medical School
  58. Riklin Raviv, Tammy, MIT, CSAIL
  59. Ruiz, Marco, UCSD
  60. Schroeder, William, Kitware
  61. Scully, Mark, The Mind Research Network
  62. Sharp, Greg, MGH
  63. Shi, Yundi, UNC Chapel Hill
  64. Shusharina, Nadya, MGH
  65. Smith, Gareth, Wolfson Medical Imaging Centre (WMIC)
  66. Souhait, Lydie, Harvard Medical School
  67. Spinczyk, Dominik, Silesian University of Technology
  68. Srinivasan, Padmapriya
  69. Tao, Xiaodong, GE Research
  70. Ungi, Tamas, Queen's University
  71. Vachet, Clement, UNC Chapel Hill
  72. Veni, Gopalkrishna, SCI Institute
  73. Wassermann, Demian, SPL/LMI/PNL
  74. Wells, Sandy, BWH
  75. Wu, Guorong, University of North Carolina at Chapel Hill
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