Difference between revisions of "2010 Summer Project Week"

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(Microscopy Image Analysis)
(Microscopy Image Analysis)
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===[[Microscopy Image Analysis]] ===
 
===[[Microscopy Image Analysis]] ===
* [[2010 Project Week DICOM supplement 145 | DICOM supplement 145]] (see [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf here]: Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
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* [[2010 Project Week DICOM supplement 145 | DICOM supplement 145]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
 
* [[ Microscopy extensions for ITK]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
 
* [[ Microscopy extensions for ITK]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
 
* [[ Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)
 
* [[ Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)

Revision as of 00:14, 14 June 2010

Home < 2010 Summer Project Week


Back to Project Events, Events

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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

    • 8:30am breakfast
    • 10am-noon: Project Progress Updates
      • Noon: Lunch boxes and adjourn by 1:30pm.
      • We need to empty room by 1:30. You are welcome to use wireless in Stata.
      • Please sign up for the developer mailing lists
      • Next Project Week in Utah

Projects

Segmentation

Registration

IGT

Radiotherapy

Analysis

  • Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
  • Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
  • MRSI module and SIVIC interface (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
  • Automatic SPHARM Shape Analysis in 3D Slicer (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

Microscopy Image Analysis

Shape Analysis

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. Nicole Aucoin , BWH
  2. Michel Audette , Kitware
  3. Stephen Aylward , Kitware, Inc
  4. Alexis Boucharin , UNC Neuro Image Research and Analysis Laboratories
  5. Sylvain Bouix , BWH
  6. Michael Bowers , Johns Hopkins University
  7. Francois Budin , UNC
  8. Everette Burdette , Acoustic MedSystems, Inc.
  9. Laurent CHAUVIN , Brigham and Women's Hospital
  10. Min Chen , Johns Hopkins University
  11. Jason Crane , UCSF
  12. Manasi Datar , SCI Institute
  13. Liya Ding , The Ohio State University
  14. Ryan Eckbo , BWH
  15. Ilker Ersoy , University of Missouri Columbia
  16. Andriy Fedorov , Surgical Planning Lab
  17. Jean-Christophe Fillion-Robin , Kitware Inc.
  18. Julien Finet , Kitware Inc
  19. James Fishbaugh , SCI Institute
  20. Karl Fritscher , UMIT
  21. Yi Gao , Gerogia Tech
  22. Arnaud GELAS , Harvard Medical School
  23. Chris Gorgolewski , SPL
  24. alexandre gouaillard , CoSMo Software
  25. Sylvain Gouttard , SCI Institute
  26. Kedar Grama, Rensselaer Polytechnic Institute
  27. Daniel Haehn , University of Pennsylvania
  28. Adel Hafiane , ENSI-Bourges
  29. Nathan Hageman ,
  30. Dieter Hahn , University Erlangen
  31. Michael Halle , BWH/SPL
  32. Corentin Hamel , UNC Chapel Hill
  33. Nobuhiko Hata , Brigham and Women's Hospital
  34. Kathryn Hayes , Brigham and Women's Hospital
  35. Nicholas Herlambang , AZE, Ltd.
  36. Leslie Holton , Medtronic Navigation
  37. Luis Ibanez , KITWARE Inc.
  38. Jayender Jagadeesan , SPL
  39. Hans Johnson , University of Iowa
  40. Tina Kapur , Brigham and Women's Hospital
  41. Ron Kikinis , Brigham and Women's Hospital
  42. Minjeong Kim , UNC-Chapel Hill
  43. Ivan Kolesov , Georgia Institute of Technology
  44. Garrett Larson , UNC-CH
  45. Rui Li , MGH
  46. Curtis Lisle , KnowledgeVis, LLC
  47. Haiying Liu , Brigham and Women's Hospital
  48. Yanling Liu , SAIC-Frederick, Inc.
  49. Bradley Lowekamp , Lockheed Martin
  50. raghu machiraju , The Ohio State University
  51. Vincent Magnotta , The University of Iowa
  52. mathieu malaterre , CoSMo Software
  53. Daniel Marcus , Washington University
  54. Katie Mastrogiacomo , Brigham and Women's Hospital
  55. Joy Matsui , University
  56. Sean Megason , Harvard Medical School
  57. Dominik Meier , BWH, Boston MA
  58. bjoern menze , CSAIL MIT
  59. Mikhail Milchenko , WUSTL
  60. James Miller , GE Research
  61. Kishore Mosaliganti , Harvard Medical School
  62. Marc Niethammer , UNC Chapel Hill
  63. Isaiah Norton , BWH Neurosurgery
  64. Raghav Padmanabhan , RPI
  65. Kannappan Palaniappan , university of Missouri
  66. Beatriz Paniagua , University of North Caolina at Chapel Hill
  67. Xenophon Papademetris , Yale University
  68. David Partyka , Kitware Inc
  69. Pratik Patel ,
  70. Sudhir Pathak , Univeristy Of Pittsburgh
  71. Marta Peroni , Politecnico di Milano
  72. Antonin Perrot-Audet , Harvard Medical School
  73. Steve Pieper , Isomics, Inc.
  74. Wendy Plesniak , BWH
  75. Kilian Pohl , IBM
  76. Sonia Pujol , Brigham and Women's Hospital
  77. Nicolas Rannou , Harvard Medical School
  78. Tammy Riklin Raviv , MIT, CSAIL
  79. Marco Ruiz , UCSD
  80. William Schroeder , Kitware
  81. Mark Scully , The Mind Research Network
  82. Greg Sharp , MGH
  83. Yundi Shi , UNC Chapel Hill
  84. Nadya Shusharina , MGH
  85. Shantanu Singh , The Ohio State University
  86. Gareth Smith , Wolfson Medical Imaging Centre (WMIC)
  87. Lydie Souhait , Harvard Medical School
  88. Dominik Spinczyk , Silesian University of Technology
  89. Padmapriya Srinivasan ,
  90. Xiaodong Tao , GE Research
  91. Junichi Tokuda , Brigham and Women's Hospital
  92. Tamas Ungi , Queen's University
  93. Clement Vachet , UNC Chapel Hill
  94. Gopalkrishna Veni , SCI Institute
  95. Demian Wassermann , SPL/LMI/PNL
  96. Adam Weinrich , Nokia
  97. Sandy Wells , BWH
  98. Guorong Wu , University of North Carolina at Chapel Hill
  99. Alexander Yarmarkovich , ISOMICS
  100. Alexander Zaitsev , Brigham and Womens Hospital