January 2012 – Kitware News II

January 27, 2012

VisWeek 2011
For the tenth straight year, Kitware sponsored VisWeek, the premier forum for advances in scientific and information visualization. The team was very active at this conference, presenting papers, participating in panel discussions, and meeting with collaborators. Jeff Baumes presented the paper “Geospatial and Entity Driven Document Visualization for Non-Proliferation Analysis” as part of the Workshop on Interactive Visual Text Analytics for Decision Making. Will Schroeder spoke as part of the “Verification in Visualization: Building a Common Culture” panel with Robert Kirby, Claudio Silva, and Robert Laramee.

The team was also busy giving demonstrations of Kitware’s new VTK OpenGL ES Rendering Toolkit (VES) and KiwiViewer, the mobile visualization app for geometric data.

ParaView at 2011 LDAV Symposium
This year’s IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV), held in conjunction with VisWeek, included a number of presentations highlighting customizations and extensions of ParaView.

Joe Insley discussed how he and his team used ParaView to develop visualization tools for data coupled from continuum-atomistic simulations in the paper “Visualizing Multiscale, Multiphysics Simulation: Brain Blood Flow”.

Venkat Vishwanath presented “Toward Simulation-Time Data Analysis and I/O Acceleration on Leadership-class Systems,” highlighting work on GLEAN, a flexible framework for data-analysis and I/O acceleration at extreme scales, and ParaView’s coprocessing capabilities. Also speaking to coprocessing was Nathan Fabian who presented “The ParaView Coprocessing Library: A Scalable, General Purpose In Situ Visualization Library”. Fabian presented results from integrating the library into various simulations codes, such as PHASTA, CTH, and S3D.

John Patchett presented the paper “Revisiting Wavelet Compression for Large-Scale Climate Data using JPEG 300 and Ensuring Data Precision,” by Jon Woodring, et al. The paper argued that the majority of data bottlenecks  are due to data movement associated with bandwidth limitations. Using ParaView, the team developed reader plugins, new streaming views, and enhancements for the VTK pipeline.

HPC Consortium Discussion of Open Source
Bob O’Bara and Andy Bauer attended the High Performance Computing Consortium at Rensselaer Polytechnic Institute in Troy, NY.  

ParaView was highlighted in a few different presentations, hitting on topics such as CFD simulation by Cameron Smith of SCOREC and RPI, and massively parallel CFD using anisotropic grids by Ken Jansen and Onkar Sahni. Kirk Jordan, Program Director of the Computational Science center IBM Waston, discussed the use of ParaView Web as a good example of making HPC functionalities more accessible.

During a panel that focused on HPC software, audience members chimed in to comment on merits of open source tools in comparison to current prohibitive pricing models for commercial products.  Based on some of the responses made by vendors and academics, there seems to be an incorrect perceived notion that open source tools are fragile and hard to use. Despite great advances in recent years, the open source community still has obstacles to overcome when it comes to winning over commercial HPC users and advocates.

Stephen Aylward, Brad Davis, Andinet Enquobahrie, Luis Ibanez, Danielle Pace, and Matt McCormick were actively involved in the 14th annual International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI) in Toronto this October.

Andinet led a systems and architectures workshop on computer-assisted interventions. Danielle Pace presented “Sliding Geometries in Deformable Image Registration” as part of the Abdominal Imaging workshop. Luis led tutorials on ITKv4, and SimpleITK along with Daniel Blezek of the Mayo Clinic.

Stephen Aylward acted as co-chair for oral presentations was a co-author on the paper “Geometric Metamorphosis,” along with Marc Niethammer, Gabriel L. Hart, Danielle F. Pace, Paul M. Vespa, Andrei Irimia, and John D. Van Horn. Marc Niethammer presented the paper.

The team also participated in the student event “Your Career in Industry and Academia,” an informal interactive session for students to discuss career opportunities in each arena.

Kitware also sponsored the Young Scientist Publication Impact Award, which recognizes scientists who are early in their careers and are shaping the medical image analysis field. We commend Dr. Boon Thye Yeo who received the inaugural award for his paper “Effects of Registration  Regularization and Atlas Sharpness on Segmentation Accuracy.” Honorable mentions went to Dr. Kang Li for his paper, “Cell Population Tracking and Lineage Construction with Spatiotemporal Context” and Dr. Paul M. Novotny for his paper “GPU Based Real-time Instrument Tracking with Three Dimensional Ultrasound.”

Kitware Participates in RSNA 2011
Kitware attended RSNA in Chicago, where we met with collaborators, demonstrated our newest work, taught workshops and participated in exhibits.

We taught two courses, “Open Source Applications for Medical Imaging Research” and “Introduction to Open-Source Software Libraries for Medical Imaging”. These courses were sold-out with more than 100 attendees and received high acclaim.

The open-source libraries course spoke to several open-source software libraries used in medical imaging, including VTK, ITK, Midas, and VES. We discussed the rigorous software processes used to ensure stability in the toolkits and specific use case applications for medical imaging. Participants were engaged with live demonstrations of coding of SimpleITK and new features of VES.

We also had two exhibits in the Quantitative Imaging Reading Room (QIRR): “3D Slicer: An open-source software platform for segmentation, registration, quantitative analysis and 3D visualization of biomedical image data,” a collaborative exhibit with NA-MIC, and “Understanding and Improving CT Image Quality With Automated Pocket Phantom Technology.”

New Employees
Jason Li
Jason Li joined the medical team at Kitware’s Clifton Park office in October. He holds a maser’s degree in computer science from the University of Kentucky at Lexington and a bachelor’s degree in mechanical engineering from Beijing Jiao Tong University in China.

Kyle Lutz
Kyle Lutz joined the scientific visualization team at the Clifton Park office in June 2011. He holds a bachelor’s of science in biology from the University of California, Santa Barbara.

Roland Kwitt
Dr. Roland Kwitt joined the Kitware team at the Carrboro office in December. He holds a Ph.D. in computer science from the University of Salzburg in Austria, where he also received his masters of science and taught classes on network management and object oriented programming.

Philippe Pébay
Dr. Philippe Pébay joined Kitware SAS in Lyon, France in October as Director of Visualization and High Performance Computing. He holds a Ph.D. in applied mathemathics from the Universite Pierre er Marie Curie in Paris.

Jérôme Velut
Dr. Jérôme Velut joined Kitware SAS in Lyon, France in November. He recently completed a post-doctoral fellowship in medical imaging from the University of Rennes after receiving his Ph.D. in information processing from the National Institute for Applied Science (INSA) in Lyon.

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