Difference between revisions of "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 and traveled to the project week from 10 countries (US, Austria, Singapore, France, Germany, Japan, Italy, England, Poland, and Canada). Within the US, participants traveled to project week from 16 states (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.

Summer 2010 Project Week
Volume Rendering Breakout Session
Raise Your Hand if you are a NRRD
Hard at Work
Brainlab VVlink OpenIGTLink Demo
Tutorial Contest Presentation

More Photos

Projects

Segmentation

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

Registration

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

Shape Analysis

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

Analysis

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

Microscopy Image Analysis

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 )
Import/Export Farsight-GoFigure results (Arnaud Gelas, Lydie Souhait, Kedar Grama, Raghav Padmanabhan, Sean Megason, Badri Roysam)
JPEG2000 and HDF5 Image Readers in ITK (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
ITK Spherical Harmonics filter for shape analysis of cell nuclei (Shantanu Singh, Kishore Mosaliganti, Arnaud Gelas, Sean Megason, Raghu Machiraju)
ITK Analysis of Large Histology Datasets (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
CTK Transfer function widget (Nicolas Rannou, Julien Finet, Arnaud Gelas, Stever Pieper)
Seedings results comparison (Antonin Perrot-Audet, Raghav Padmanabhan, Kishore Mosaliganti, Badri Roysam, Sean Megason)
ITK Multiphase and GPAC level sets (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
Median binary pattern texture measures for cell nuclei segmentation (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
Standards and Interfaces for Microscopy Image Analysis in ITK (whoever has an opinion, Sean Megason)

NA-MIC Kit Internals

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

Workflows and Integration

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:

We need to empty room by 1:30pm on Friday. You are welcome to use wireless in Stata.
Please sign up for the developer mailing lists
Next Project Week January 3-7, 2011, Salt Lake City, Utah

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

Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
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!
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.
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)
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...
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.

Yousef Al-Kofahi , CompuCyte Corporation
Peter Anderson , retired
Nicole Aucoin , BWH
Michel Audette , Kitware
Stephen Aylward , Kitware, Inc
Jim Barabas, MIT
Barrett, Ryan, BWH
Alexis Boucharin , UNC Neuro Image Research and Analysis Laboratories
Sylvain Bouix , BWH
Michael Bowers , Johns Hopkins University
Francois Budin , UNC
Everette Burdette , Acoustic MedSystems, Inc.
Laurent CHAUVIN , Brigham and Women's Hospital
Min Chen , Johns Hopkins University
Jason Crane , UCSF
Nikos Chrisochoides, College of William and Mary
Manasi Datar , SCI Institute
Liya Ding , The Ohio State University
Ryan Eckbo , BWH
Ilker Ersoy , University of Missouri Columbia
Andriy Fedorov , Surgical Planning Lab
Jean-Christophe Fillion-Robin , Kitware Inc.
Julien Finet , Kitware Inc
James Fishbaugh , SCI Institute
Karl Fritscher , UMIT
Yi Gao , Gerogia Tech
Arnaud GELAS , Harvard Medical School
Randy Gollub , MGH
Chris Gorgolewski , SPL
alexandre gouaillard , CoSMo Software
Sylvain Gouttard , SCI Institute
Kedar Grama , Rensselaer Polytechnic Institute
Daniel Haehn , University of Pennsylvania
Adel Hafiane , ENSI-Bourges
Nathan Hageman ,
Dieter Hahn , University Erlangen
Michael Halle , BWH/SPL
Corentin Hamel , UNC Chapel Hill
Nobuhiko Hata , Brigham and Women's Hospital
Kathryn Hayes , Brigham and Women's Hospital
Nicholas Herlambang , AZE, Ltd.
Masakatsu Hoashi, AZE Ltd.
Leslie Holton , Medtronic Navigation
Luis Ibanez , KITWARE Inc.
Jayender Jagadeesan , SPL
Hans Johnson , University of Iowa
Tina Kapur , Brigham and Women's Hospital
Peter Karasev, Georgia Tech
Ron Kikinis , Brigham and Women's Hospital
Minjeong Kim , UNC-Chapel Hill
Ivan Kolesov , Georgia Institute of Technology
Garrett Larson , UNC-CH
Joohwi Lee , UNC Chapel Hill
Rui Li , MGH
Stefan Lienhard , LMI
Curtis Lisle , KnowledgeVis, LLC
Haiying Liu , Brigham and Women's Hospital
Felix Liu , Beth Israel Deaconess Medical Center
Yanling Liu , SAIC-Frederick, Inc.
Bradley Lowekamp , Lockheed Martin
raghu machiraju , The Ohio State University
Vincent Magnotta , The University of Iowa
mathieu malaterre , CoSMo Software
Charles Maneval, BWH
Daniel Marcus , Washington University
William Marks , Focused Ultrasound Lab, BWH, HMS
Katie Mastrogiacomo , Brigham and Women's Hospital
Joy Matsui , University
Sean Megason , Harvard Medical School
Dominik Meier , BWH, Boston MA
bjoern menze , CSAIL MIT
Mikhail Milchenko , WUSTL
James Miller , GE Research
Kishore Mosaliganti , Harvard Medical School
Marc Niethammer , UNC Chapel Hill
Isaiah Norton , BWH Neurosurgery
Beck Olson , UCSF
John Onofrey , Yale University
Raghav Padmanabhan , RPI
Kannappan Palaniappan , university of Missouri
Beatriz Paniagua , University of North Caolina at Chapel Hill
Xenophon Papademetris , Yale University
Eun-Joo Park , Brigham & Women's Hospital
David Partyka , Kitware Inc
Pratik Patel ,
Sudhir Pathak , Univeristy Of Pittsburgh
Thierry PECOT , Ohio State University
Marta Peroni , Politecnico di Milano
Antonin Perrot-Audet , Harvard Medical School
Steve Pieper , Isomics, Inc.
Wendy Plesniak , BWH
Kilian Pohl , IBM
Sonia Pujol , Brigham and Women's Hospital
Nicolas Rannou , Harvard Medical School
Tammy Riklin Raviv , MIT, CSAIL
Marco Ruiz , UCSD
Johannes Schick , SPL
William Schroeder , Kitware
Mark Scully , The Mind Research Network
Gunasekaran Seetharaman, US Air Force Research Lab
Greg Sharp , MGH
Yundi Shi , UNC Chapel Hill
Nadya Shusharina , MGH
Shantanu Singh , The Ohio State University
Gareth Smith , Wolfson Medical Imaging Centre (WMIC)
Lydie Souhait , Harvard Medical School
Dominik Spinczyk , Silesian University of Technology
Padmapriya Srinivasan ,
Xiaodong Tao , GE Research
Matthew Toews , Brigham and Women's Hospital, Harvard Medical School
Junichi Tokuda , Brigham and Women's Hospital
Tamas Ungi , Queen's University
Clement Vachet , UNC Chapel Hill
Veda Vadyar , Brigham and Women's Hospital
Gopalkrishna Veni , SCI Institute
Stuart Wallace , Massachusetts General Hospital
Demian Wassermann , SPL/LMI/PNL
Yihan Wei, BWH
Adam Weinrich , Nokia
Sandy Wells , BWH
Phillip White , BWH/HMS
Guorong Wu , University of North Carolina at Chapel Hill
Yin Wu , Mass General Hospital
Atsushi Yamada , Nagoya Institute of Technology
Alexander Yarmarkovich , ISOMICS
Alexander Zaitsev , Brigham and Womens Hospital

Revision as of 01:05, 30 June 2010 (view source) Tkapur (talk \| contribs) ← Older edit		Revision as of 13:47, 1 July 2010 (view source) Tkapur (talk \| contribs) Newer edit →
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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. The projects, agenda, and affiliations of attendees are detailed below.'''	+	'''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 and traveled to the project week from 10 countries (US, Austria, Singapore, France, Germany, Japan, Italy, England, Poland, and Canada). Within the US, participants traveled to project week from 16 states (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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Difference between revisions of "2010 Summer Project Week"

Revision as of 13:47, 1 July 2010

Projects

Segmentation

Registration

Shape Analysis

Diffusion

IGT

Radiotherapy

Analysis

Microscopy Image Analysis

NA-MIC Kit Internals

Workflows and Integration

Agenda

Background

Logistics

Preparation

Attendee List

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