July 2012 – Kitware News

July 13, 2012

Kitware Hosts IEEE SciVis Contest Data
Kitware is hosting the IEEE SciVis Contest 2012 data on an installation of Midas, Kitware’s open-source toolkit that enables the rapid creation of tailored, web-enabled data storage. It is optimized for efficiently centralizing, indexing, and storing massive collections of data, providing the foundation for computational scientific research.

In this regard, Midas is perfect for supporting this year’s IEEE SciVis contest, which targets the field of computational material science, particularly atomic configurations. The goal of this year’s contest, part of IEEE VisWeek 2012, is to devise a visualization that allows for exploring the phase transitions of a particular ferroelectric material while decreasing the temperature gradually.

A repository with this and previous years’ contest data is available in easily-navigable communities. Further contest details and the public data for the contest are available at http://midas3.kitware.com/midas/community/1#tabs-info.

InnerOptic and Kitware Collaboration
InnerOptic Technology and Kitware announced NIH Phase II SBIR funding for the development of a needle guidance system for hepatic tumor ablation. The operating room ready system will provide novel 3D visualizations for needle guidance in soft tissues. Brian Heaney is the PI and will lead and oversee the project at InnerOptic, and Stephen Aylward will lead the Kitware effort.

Using InnerOptic’s Spotlight™ technology, which was developed during Phase I of this grant, intra-operative ultrasound images will be fused with pre-operative computed tomography (CT) images. The Spotlight system renders opaquely and in sharp detail only the portions of the CT data that are in the vicinity of the ultrasound probe or the needle trajectory. This is analogous to a spotlight on stage: illuminating the scene of interest, while the rest of the stage is transparent and out-of-focus to be less distracting.

During liver lesion ablations and other image-guided procedures, surgeons and interventional radiologists currently must rely on mentally-integrated information from several imaging modalities. While CT imaging has excellent diagnostic value, breathing and surgical manipulation can cause tissues to move and deform. Additionally, intra-operative ultrasound images are available in real-time but have a limited field-of-view and can be less effective than CT at distinguishing tissues and pathologies. Physicians must therefore alternate between viewing annotated pre-operative CT images or live ultrasound images on separate monitors, with no interaction between them. The awarded Phase II grant will extend Spotlight with registration algorithms that will keep the CT and ultrasound images continuously aligned. The work will result in a radically improved workflow for using CT and ultrasound images in image-guided soft tissue procedures.

National Institutes of Health Acknowledgement and Disclaimer: Research reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under Award Number R44CA143234. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Kitware Wins Three DOE SBIR Awards
In April, Kitware announced $450,000 in Department of Energy SBIR Phase I awards. The awards will fund three projects focused on scientific computing: “In-Situ Analysis of Cosmology Data,” “Cloud Computing and Visualization Tools for KBase,” and “Graphical HPC Application Suite for Supporting the Product Simulation Lifecycle.”

This DensityProfile shows the set of concentric spheres centered at each halo center and DensityProfilePlot
shows the corresponding particle density, i.e., number of particles, within each sphere.

In-Situ Analysis of Cosmology Data
Dr. Berk Geveci will lead the development of a cosmology analysis framework for in-situ analysis and data-reduction of cosmological simulations. Such simulations play an important role in the DOE’s High Energy Physics Cosmic Frontier program and are critical for understanding dark energy. This project requires an evolutionary shift in the way cosmological predictions are obtained, and therefore addresses critical challenges such as workflow I/O and the lack of domain-specific data analysis algorithms. An infrastructure will be developed that provides data reduction for minimizing input and output, robust and efficient halo-extraction methods, online tracking of halos to capture halo formation dynamics, and in-situ and co-visualization capabilities.

The voronoi tesselation used in identifying voids in cosmological simulations. This is being developed by Peterka et al. (http://www.mcs.anl.gov/uploads/cels/papers/P2087-0512.pdf)

In addition to its use in cosmology simulations, the developed framework will have wide applicability in industries that use particle-based simulation techniques, including astrophysics, ballistics and defense, volcanology, oceanology, solid mechanics modeling, and a range of maritime applications. The adaptability of this framework for use with large-data simulations will drive new levels of innovation in the computational sciences and facilitate the necessary transition from terascale work to peta- and exascale computing.

Cloud Computing and Visualization Tools for KBase
Dr. Jeffrey Baumes will lead the work focused on the DOE’s Systems Biology Knowledgebase (Kbase), a community-driven cyberinfrastructure for sharing and integrating biology and genetics data. Kitware will collaborate with The Ohio State University on this project, which will specifically address the critical need of extracting meaningful knowledge from ever-growing volumes of scientific data by making improvements to Kbase. Three distinct improvements will be made to Kbase: the design and incorporation of a new cloud-based architecture for genetics algorithms, integration of new visualization tools, and the ability to link algorithms to existing databases.

A fully functional, visualization-enabled Kbase system could be adopted by genetics and systems biology laboratories at academic, government, and industrial research centers due to its customizable, open-source nature. Organizations can use the system to deploy their own components and efficiently produce, share, and run their algorithms from the cloud, providing easy collaboration with researchers from both within and outside of the agency.

Graphical HPC Application Suite for Supporting the Product Simulation Lifecycle
Bob O’Bara will lead the HPC application suite project, which will focus on enabling widespread adoption of high performance computing (HPC) functionality for small and medium-sized manufacturing firms by providing a suite of open-source applications that address the complete simulation lifecycle. The project will address current hurdles of technology integration, interaction, and scalability. Many of the current tools used to address parts of the simulation lifecycle are rigid, expensive, and cumbersome for non-simulation experts; Kitware’s open-source solution will make it more realistic for organizations of all sizes and budgets to leverage HPC resources.

Simulation lifecycle using conceptual scenarios

The project will address these issues and streamline manufacturing workflows by developing a suite of open-source applications based on a flexible framework and built upon existing open-source HPC toolkits such as CGM, OpenCASCADE, MOAB, Meshkit, and ParaView. This project will specifically target the field of computational fluid dynamics; however, the applications are interchangeable, customizable, and can be easily modified to address various vertical markets. A consistent, intuitive graphical user interface will be used in the different applications in the suite, making it easy to use by experts and non-experts alike.

Kitware Collaborates on SDAV Institute
Kitware is a collaborating team member in the Scalable Data Management, Analysis, and Visualization (SDAV) Institute, supported by the U.S. Department of Energy’s Scientific Discovery through Advanced Computing (SciDAC) program. The project, led by Lawrence Berkeley National Lab, is a collaboration between prominent government laboratory, university, and industry partners for the purpose of creating a comprehensive set of tools and techniques that are essential for knowledge discovery on the DOE’s various computing platforms over the next five years.

The SDAV Institute’s primary goals are to actively work with application teams and assist them in achieving breakthrough science; and to provide technical solutions in data management, analysis, and visualization, all of which are broadly used by the computational science community. Such expertise is required to address the ever-increasing size, scale, complexity, and richness of scientific data.

Current users of DOE computing systems are faced with managing and analyzing their datasets for knowledge discovery, and must often rely on antiquated tools more appropriate for the teraflop era. While new techniques for interpreting large data have been developed, many in the field believe that these new algorithms and implementations will not work on their systems as we move into the many-core era. Without addressing these issues and beliefs, there will be a widening gap between computational and I/O capacity.

The SDAV Institute is working with DOE researchers to develop a comprehensive approach that will address these issues by encompassing all the stages of data analysis from initial data generation, orchestration of analysis tasks, and effective visualization of the results.

Kitware is supporting the DOE’s scientific teams with large-scale data analysis and visualization. This involves making enhancements and extensions to current tools, such as ParaView and VisIt; introducing and supporting new technologies leveraging many-core and multi-core architectures; and coupling data analysis capability with simulation codes for in-situ analysis and co-processing.

Tom Munnecke Visits Kitware
In April, Kitware hosted Tom Munnecke, one of the world’s leading experts in health information technology and an original member of the VistA team, who gave a presentation titled “Towards a Federal Health Information Space.” He discussed his observations and lessons learned as one of the original architects of VistA and CHCS, and focused on the need for an open, adaptable health information space. To this end, he presented an architectural conceptual model based on an “Information Space” rather than a “Integrated System” that approaches the federal health information as a large-scale, fine-grained network of information and interactions. His recorded presentation is available on Kitware’s webinar page, www.kitware.com/products/webinars.html.

Kitware Participates in the University at Albany Open Source Festival
Will Schroeder, Bill Hoffman, and Luis Ibáñez presented at the University at Albany Open Source Festival in March. The event, organized by the UAlbany Student Chapter of the American Society for Information Science & Technology (ASIS&T), brought together many groups invested in open source, along with others interested in learning more about the Way of the Source.

Will gave a presentation titled “Open Source Business Models,” during which he spoke about the variety of business models that have been used to monetize open-source software and communities. Will discussed a variety of business approaches ranging from open source as a hobby to consulting, dual licensing, and collaborative R&D, which is a major component of the Kitware model.

Bill presented on “Open Source Quality Processes” and discussed how open-source practices result in higher-quality software due to the many eyes theory. Although not all open-source projects will benefit from this theory as much as the Linux kernel, there are open tools and processes that enable developers to share and test software regardless of community size. Tools including Git, CMake, CTest, and CDash are examples of freely-available tools for managing, building, and testing high-quality software – while also reducing maintenance costs and maximizing community involvement.

Lastly, Luis Ibáñez gave two presentations, one on “Open Source in Healthcare” and another focused on “Open Source in Education”. In speaking on open source in healthcare, Luis introduced the economic relevance of healthcare costs in the U.S. He described how the open-source community can contribute to reducing the cost of healthcare while simultaneously increasing its quality by participating on the open-source initiatives surrounding the development of electronic health record (EHR) systems, such as the Veterans Health Information Systems and Technology Architecture (VistA) and the open-source EHR Agent (OSEHRA).

In the “Open Source in Education” talk, Luis presented on how Kitware has partnered with Rensselaer Polytechnic Institute (RPI) since 2007 to offer an Open Source Software Practices class. In this class, students are exposed to basic principles of economics; models of peer-production; social principles of collaboration; the legal basis of copyrights, patents, and trademarks; principles of software licensing; and the motivational aspects of cooperation. Simultaneously, students are able to practice interaction skills with open-source communities through use of revision control systems, mailing lists, forums, wikis, code peer-review systems, software quality control, and documentation.

Kitware to Open New Mexico Office
In mid-June, Kitware announced the opening of our third U.S.-based office in Santa Fe, New Mexico. The office will be headed by Patrick O’Leary, a specialist in high performance computing, who will be leading the office as Assistant Director of Scientific Computing. Before joining Kitware, Dr. O’Leary was the Director of the Center for Advanced Modeling and Simulation at Idaho National Laboratory; as well as Director of Operations of WestGrid, one of the seven partner consortia that make up Compute Canada.

Similar to Kitware offices in Clifton Park, NY; Carrboro, NC; and Lyon, France, the new location will provide support and services for scientific computing, particularly focused on high performance computing and visualization.
“I could not be more excited about this venture,” said Dr. O’Leary. “New Mexico is a great location to focus on HPC and visualization as the National Labs there are leading the field. With this expansion, Kitware will now be able to provide more direct support and consulting to these organizations.”

“Kitware recognizes the increasing importance of computational science, analytics, and large data, and the necessity of growing our HPC capabilities,” said Will Schroeder. “We are thrilled to have Dr. O’Leary on our team and are looking forward to exploring new collaboration opportunities that help us impact and improve scientific research.”

ISBI 2012: ITK-focused Hackathons
Kitware attended the International Symposium on Biomedical Imaging (ISBI) and participated in two ITK-related hackathons: integrating the NiftyReg library from University of College of London into ITK and integrating more ITK functionalities into Osirix. Over the two days of hackathons, Luis Ibáñez, Xiaoxiao Liu, and Matt McCormick met with several group to discuss ITK, new ideas, and potential collaborations.

The NiftyReg hackathon focused on integrating the NiftyReg tool as an ITK module. NiftyReg is a package that performs Image Registration by taking advantage of GPUs. The NA-MIC / Slicer community has been interested in using this library; by including it as an external ITK module, it will be easier for the NA-MIC and ITK communities in general to get take advantage pf NiftyReg. The proposed course of action for the ITK team includes assisting with the configuration of an external module and testing.

In the Osirix hackathon, Kitwareans worked with Jan Perhac from the Osirix team in Geneva and two researchers from the Polytechnic University of Catalunya (UPC): Raul Benitez and Oriol Carrillo. The hackathon focued on building an example ITK plugin for Osirix and discussing using ITK pipelines in Osirix for  Image Guided Surgery (IGS) applications. The Osirix team explained that the plugin infrastructure is in flux, but that once it is settled, there will be abundant opportunities for extending Osirix via ITK, IGSTK, and TubeTK plugins.

Kitware Announces Spring Promotions
This spring, Kitware announced several promotions of its team members. Theresa Vincent is now an Accounting Administrator in recognition of her growing authority and responsibility in driving the Accounts Payable operations. There are two new Technical Experts, Brad King and Roddy Collins, recognizing them as individuals who have made and continue to make sustained and broad technical impacts across Kitware. Kitware also promoted two new Technical Leaders,  Patrick Reynolds and Marcus Hanwell, acknowledging their  contributions to building cross-cutting technology and developing a new initiative in computational chemsitry, respectively. Lastly, Anthony Hoogs was promoted to Senior Director of Computer Vision for his significant contributions to Kitware, and Stephen Aylward was promoted to Senior Director of Operations – North Carolina for his work in growing and managing the North Carolina office. Congratulations to the Kitwareans on their achievements!

Upcoming Conferences and Events
OSCON 2012
July 16-20 in Portland, OR. Kitware will give two presentations at the event, “Mobile 3D Visualization” and “OSEHRA – Building an Open Source EHR for All.”
July 16-21 in Austin, TX. Matthew McCormick is co-chairing the program committee for the 11th annual Scientific Computing with Python Conference.
August 5-9 in Los Angeles, CA.
American Chemical Society Meeting
August 19-23 in Philadelphia, PA. Marcus Hanwell and Kyle Lutz will present two talks, “Avogadro, Open Chemistry and Chemical Semantics” and “Exploring Large Chemical Data Sets: Interactive Analysis and Visualization.”  
BioImage Informatics
September 16-19 in Dresden, Germany. Luis Ibáñez , an invited speaker, will present a talk titled “Reproducible Image Analysis for Research and Education.”
October 1-5 in Nice, France. Kitware will sponsor the “Young Scientist Publication Impact” award.
SIAM Conference on Mathematics for Industry
October 2 in Denver, CO. Will Schroeder is a plenary speaker and will present a talk focused on the value of leading-edge visualization for industrial research and development.

New Employees
David Lonie
David Lonie joined Kitware as an R&D Engineer on the scientific computing team at the Clifton Park office. David is completing his Ph.D. in chemistry at the State University of New York at Buffalo, where his thesis focuses on the evolutionary algorithm prediction of novel crystalline structures.

Patrick O’Leary
Patrick O’Leary joined Kitware as the Assistant Director of Scientific Computing and leader of Kitware’s newest office in Santa Fe, New Mexico. Dr. O’Leary’s expertise includes large-scale scientific computing, visualization, and modeling; high performance computing, and leadership.

Kevin Zimmerman
Kevin Zimmerman joined Kitware as a Systems Administrator at the Clifton Park office, bringing more than 17 years of experience to the team. Kevin earned his M.S. degree in management with an MIS concentration from Rensselaer Polytechnic Institute in Troy, NY.

Ricardo Ortiz
Ricardo Ortiz joined the medical team as an R&D Engineer at the Carrboro office. He earned his Ph.D. in applied mathematics and computational sciences from the University of Iowa. Ricardo is also a Postdoctoral Fellow Associate in the mathematics department at the University of North Carolina at Chapel Hill.

kitware internships
Kitware is pleased to welcome ten new and returning interns this summer. The five interns at the Clifton Park office are assisting the computer vision and medical teams and include Ilseo Kim, Tianyang Ma, Sean Tozier, Syed Zain Masood, and Dan Gnoutcheff.

At the Carrboro office, Vikas Shivaprabhu, Christopher Mullins, and Nathan Taylor are assisting the computer vision and medical teams. Célia Pansard and Guillaume Sala are long-term interns and will be with Kitware for the next year.
Kitware Internships provide current college students with the opportunity to gain hands-on experience working with leaders in their fields on cutting edge problems. Our business model is based on open source software—an exciting, rewarding work environment.

Our interns assist in developing foundational research and leading-edge technology across six business areas: supercomputing visualization, computer vision, medical imaging, data management, informatics and quality software process. We offer our interns a challenging work environment and the opportunity to attend advanced software training. To apply send, your resume to internships@kitware.com.

Employment Opportunities
Kitware is seeking talented, motivated and creative individuals to fill open positions in all of our offices. As one of the fastest growing companies in the country, we have an immediate need for software developers and researchers, especially those with experience in computer vision, scientific computing and medical imaging.

At Kitware, you will work on cutting-edge research alongside experts in the field, and our open source business model means that your impact goes far beyond Kitware as you become part of the worldwide communities surrounding our projects.

Kitware employees are passionate and dedicated to innovative open-source solutions. They enjoy a collaborative work environment that empowers them to pursue new opportunities and challenge the status quo with new ideas.  In addition to providing an excellent workplace, we offer comprehensive benefits including: flexible hours; six weeks paid time off; a computer hardware budget; 401(k); health, vision, dental and life insurance; short- and long-term disability, visa processing; a generous compensation plan; yearly bonus; and free drinks and snacks. For more details, visit our employment site at jobs.kitware.com

Interested applicants are encouraged to send their cover letter and resume to jobs@kitware.com.

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