April 2013: Kitware News

April 15, 2013

National Cancer Informatics Program Open Development Initiative
Kitware is collaborating with SAIC-Frederick, Inc. (SAIC-F) to migrate a collection of National Cancer Institute (NCI)-sponsored software projects to an open-source environment in Github.

Kitware will play an advisory role in this project and provide NCI and SAIC-F personnel with knowledge, tools, and skills for successfully managing the migration process and implementing strategies for community growth and support.

The end results from this project will include a set of well-defined standard operating procedures detailing the process of migrating projects from subversion (SVN) repositories hosted at NCI to a National Cancer Informatics Program (NCIP) space hosted in Github. In-house teams at NCI and SAIC-F will be trained with skills and methodologies for fostering these communities, and applying open-source practices to existing projects funded by NCI and other supporting organizations.

LOCI Lab Workshop & Hackathon  
At the end of January, Matt McCormick traveled to the University of Wisconsin-Madison for an ITK workshop and hackathon with the Laboratory of Optical and Computational Instrumentation (LOCI) laboratory.

The objective of the hackathon was to create a Gerrit Code Review patch to the bioformats ImageIO library in ITK. A great deal of effort had already been made by Gaetan Lehmann and Mark Hiner on this bridge, but a number of remaining issues were resolved. Johannes Schindelin of MSys Git, git rebase -i, and Fiji fame also made good progress on the WebITK concept.

Matt also delivered a well-attended workshop on ITK to the broader UW-Madison community. The hands-on workshop started with an introduction to ITK and followed with exercises on SimpleITK IPython notebooks, building and running ITK examples, level set segmentation theory, registration theory, and a review of how to contribute to the ITK community.  Materials were delivered on a virtual machine, which can be downloaded from ITK’s Midas Community.

Kitware to Develop Novel Neuroimage Processing Methods for Traumatic Brain Injury
Kitware was awarded $296,676 in NIH Phase I STTR funding to develop new neuroimage processing methods for the assessment and treatment of traumatic brain injury (TBI).

Costs associated with TBI treatments exceed $60 billion a year, but existing assessment methods fall short of clinical requirements. Clinicians need informative metrics and easy-to-use image analysis tools that can handle large, heterogeneous pathologies causing severe brain deformations.

Kitware will collaborate with the University of North Carolina, Chapel Hill and the University of California, Los Angeles (UCLA) to leverage computational methods for segmenting, registering, and interpreting images that contain large and changing pathologies to better characterize injury, quantify long-term changes, predict outcomes, and support patient treatment management.

The team will perform multimodal brain image segmentation for the assessment of acute and chronic TBI for measuring damage over a period of time, develop a new deformable image registration method for identifying acute and chronic TBI and change measurement, and investigate novel TBI metrics for predicting outcomes and guiding clinical decision making using multivariate statistics. The resulting software will be made freely available for widespread use and future extension within the open-source 3D Slicer application.

Luis Ibáñez Wins People’s Choice Award on Opensource.com!
Luis Ibáñez, a Technical Leader at Kitware, was honored with a People’s Choice Award on the RedHat community website, opensource.com. His article “Join the M Revolution – M and R Programming Languages” highlights the urgency for bringing new developers into the space of healthcare IT.

Luis is a major proponent of open-source software and open development practices. In addition to his work at Kitware, which includes leading internal development of the Insight Toolkit (ITK), he is also the Director of Science and IP at the Open Source Electronic Health Record Agent (OSEHRA). The message of his article stems from his involvement with OSEHRA, for which he actively recruits community developers for the purpose of expanding and implementing the VistA EHR system nation-wide.

Luis was one of three People’s Choice Award winners out of 20 nominees. Nominations were based on having written three or more articles for the site, or for having an article that received 3,000 or more page views. In addition to this award, Luis has also joined the site as a Community Moderator.

ITK Hackathon at MINC
The ITK team continued their series of hackathons at the McConnell Brain Imaging Centre of the Montreal Neurological Institute at McGill University. The objective there was to integrate the MINC image file format into the ITK ImageIO framework as an ITKv4 module. Huge progress was made, and a successful end to the effort was marked by a working patch on ITK’s Gerrit Code Review instance.

In the course of adding the new MINCIO features, the group solved bugs discovered in the other parts of the toolkit. Interesting discussions also arose in improvement of the object factory registration system in ITK with the C++ Micro Services library.

Kitware Gives Back at the Regional Food Bank of Northeastern NY
In January, Kitwareans volunteered their time to lend a hand at the Regional Food Bank of Northeastern NY. The Regional Food Bank services 23 counties in New York State, and last year they distributed a total of 25,684,484 pounds of food.

The Kitware team sorted frozen and prepared foods, which were checked for quality and sorted for distribution at various locations. They also divided large containers or paper and plastic goods by type: paper towels, toilet paper, sandwich bags, etc. and boxed them up.

By the end of a few hours, the team accomplished a lot and was happy to know that the results of their hard work would be delivered to local communities later in the week.

Upcoming Events & Conferences
Building Qt-enabled VTK Applications Webinar
Wednesday, April 24, 2013 3:00-4:00 PM
This free webinar will teach attendees how to create fully-featured applications using VTK and Qt.

SUNY Albany Open Source Festival
Thursday, April 25, 2013; Albany, NY
Kitwareans will attend and present the following talks:
M Revolution: teaching the next generation; Raspberry Pi Happiness in a Hackspace; and Teaching Brain Anatomy with Open Source.

Open-source, Cross-platform Charting with VTK Webinar
Thursday, May 8th, 2013 11:00 AM-12:00 PM
This free webinar will teach attendees how to use VTK’s charting modules to plot and interact with non-spatially oriented datasets.

CVPR 2013
June 23rd-27th; Portland, OR
Kitware will present the paper, “A Minimum Error Vanishing Point Detection Approach for Uncalibrated Monocular Images of Man-made Environments,” by Yiliang Xu, Sangmin Oh, and Anthony Hoogs.

Quantitative Medical Imaging (QMI) Meeting
June 24th-26th; Arlington, VA
Rick Avila is the General Chair for this event.

Computer Assisted Radiology and Surgery (CARS)
June 26th-29th; Heidelberg, Germany
Andinet Equobahrie will join Kevin Cleary of Children’s Research Institute to present a tutorial on open-source software and its uses in computer-assisted surgery.

New Employees
Charles Weatherford
Charles joined the Kitware team in Clifton Park, NY as a Communications Coordinator. He most recently worked as a Production Underwriter at Farm Family Casualty Insurance.

Jamie Snape
Jamie joined the Carrboro, NC office as an R&D Engineer. He holds a Ph.D. from UNC-Chapel Hill where his dissertation focused on “smooth and collision-free navigation for multiple mobile robots and video characters.”

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