Kitware News

Kitware and UNC-Chapel Hill Receive NIH Award to Predict Stroke Outcomes

Every 40 seconds, someone in the United States has a stroke. For some stroke patients, standard therapy can lead to swift and complete recovery. For others, the same treatment can be ineffective and may even lead to further brain hemorrhage. Recent clinical research suggests that the presence of subtle brain blood vessels, known as leptomeningeal collaterals, may be a strong predictor of the effectiveness of traditional thrombolytic therapy for treating acute stroke patients; however, existing methods for detecting those vessels involve digital subtraction angiography (DSA), which is an invasive and risky procedure that requires guiding a catheter from the groin along blood vessels through the body to reach and image the vessels in the brain.

Kitware and The University of North Carolina at Chapel Hill (UNC-Chapel Hill) have teamed up to develop a computer-aided diagnosis system that automates collateral vessel status assessment using non-invasive and low-risk computed tomography angiography (CTA). To accelerate the pace of their collaboration, the National Institutes of Health (NIH) has awarded Kitware $150,000 to develop and test a prototype of Kitware’s system. The project is jointly led by Dr. Stephen Aylward, Director of Operations – North Carolina at Kitware, and Dr. Yueh Lee, a leading neuroradiologist and researcher at UNC-Chapel Hill Department of Radiology.

“This work brings together a strong yet diverse team to integrate clinical imaging with advanced image analysis algorithms and deliver a solution that can bridge research and clinical practice,” Aylward said.

The project will build on a decade of collaborative vascular modeling research at Kitware and UNC-Chapel Hill. Upon completing the effort, the team aims to present the computer-aided diagnosis system as a foundation for precision medicine research in acute stroke patients. This research can help physicians create personalized, targeted treatments by identifying subtle yet important differences between patients.

“In addition to driving acute stroke research, the project will open the door for numerous pre-clinical and clinical investigations and applications for other neurovascular conditions such as sickle cell disease, moyamoya disease, aneurysms, post-traumatic stress disorder, traumatic brain injuries, concussions, and neurodegeneration,” Aylward said.

As part of the effort, Kitware will release algorithms for vessel modeling and analysis as open-source software. This software builds on the Insight Segmentation and Registration Toolkit (ITK) and the 3D Slicer application for medical data visualization. Both ITK and 3D Slicer are freely available, open-source software that are developed and supported by Kitware and used in medical image analysis research and commercial products throughout the world.

In addition to participating in collaborative research, Kitware offers consulting services to groups that seek to build commercial systems using ITK, 3D Slicer, and Kitware’s expertise in vessel quantification and other medical technologies.

The NIH grant referenced in this statement is supported by the National Institute of Neurological Disorders and Stroke (NINDS) under Award Number R41NS086295. The content of this statement is solely the responsibility of Kitware and does not represent the official views of the NIH or NINDS.

 

Three-dimensional (3D) models of the vessels in a brain reveal the effects of a stroke.  The number and distribution of vessels are asymmetric across the hemispheres of the brain.

Kitware Makes Triangle Business Journal's Software Developer's List

Kitware placed 21st on the Triangle Business Journal's "The List: Software Developers," which ranks companies by number of employees in the Research Triangle Park. While Kitware is headquartered in Clifton Park, NY, it has expanded since it was founded in 1998 to open additional offices in Carrboro, NC; Santa Fe, NM; and Lyon, France, allowing for increased collaboration.

Kitware became part of the Research Triangle Park region in 2006 when it opened its Carrboro office. The region is widely noted for the rapid growth of cutting-edge technology firms and for being home to several universities, including Duke University, the University of North Carolina at Chapel Hill, and North Carolina State University. These elements, coupled with the vibrant cultural landscape, create an environment well-suited for innovation and collaboration.

Contributing to this environment of high-tech research, Kitware’s team is developing software technology, such as the Insight Segmentation and Registration Toolkit (ITK), to advance several fields, including quantitative image analysis. In addition to Kitware’s presence in the Research Triangle Park, the company’s work spans a global network, with customers and collaborators worldwide.

NIH Awards $1.26 Million to Kitware and Collaborators for Cancer Research

In cancer drug research, existing imaging technologies used to assess treatment response are expensive, time consuming, and difficult to operate. To overcome these challenges, the National Institutes of Health (NIH) has funded a $1.26 million small-business research project, led by Kitware, to develop a low-cost and widely applicable system for assessing cancer treatment efficacy.

The research project is centered on a novel approach to cancer detection and diagnosis that is based on using acoustic angiography to measure small changes in the microvessels that feed tumors. Acoustic angiography is a contrast-enhanced ultrasound imaging technique that is being developed by Dr. Paul Dayton at The University of North Carolina at Chapel Hill (UNC), who is a principal investigator on the project. The technique can provide unprecedented clarity in visualizing microvascular abnormalities associated with malignant cancers that resolve when those cancers respond to treatment. Although acoustic angiography is promising, manually measuring the microvessel changes that it reveals can be time consuming and prone to error.  For the research project, acoustic angiography is combined with automated vessel modeling and computer-aided diagnosis methods developed at Kitware to provide a low-cost, fast, and accurate cancer treatment monitoring system.

“The characterization of microvascular features for the diagnosis and monitoring of cancer has shown great promise, but the application of this technique has traditionally involved costly imaging equipment and highly constrained conditions,” Dr. Stephen Aylward, a principal investigator on the project and Director of Operations – North Carolina at Kitware, said. “Combining computer-aided diagnosis of microvasculature with acoustic angiography creates a powerful and practical diagnostic tool for preclinical and clinical cancer research.”

During Phase I of the project, Kitware and the Dayton Lab at UNC confirmed that the novel ultrasound-based approach can distinguish benign tumors from malignant tumors and track vascular changes throughout disease development. The team also optimized the methods for modeling and analyzing vessels so that they run in minutes, rather than hours, and offer significantly improved accuracy.

For Phase II, the team will partner with SonoVol to integrate the proposed approach into a commercial ultrasound imaging system for preclinical research. The system will provide cancer researchers with an innovative tool for studying animal models of malignancies in nearly any organ in the body. It will enable rapid alignment of images taken over time for observing longitudinal vascular remodeling and present substantial benefits over existing technologies. For example, the system will cost less than half of what traditional systems cost; it will be suitable for users who do not have expertise in imaging physics; and it will be benchtop, user agnostic, and noninvasive.

“An equivalently fast, accurate, noninvasive, low-cost, and quantitative tumor micro-environment imaging instrument does not exist,” Aylward said. “As a result, most researchers have to reserve time and expert support on shared instruments at facilities that charge extremely high fees. The proposed system will provide affordable and easy-to-use technology that could accelerate the pace of cancer research, bringing life-saving therapeutics to the patient’s bedside sooner and with a lower development cost.”

As part of the Phase II effort, Kitware will release algorithms for vessel modeling and analysis as open-source software, building on the Insight Segmentation and Registration Toolkit (ITK) and the 3D Slicer application for medical data visualization. Both ITK and 3D Slicer are freely available. They are developed and supported by Kitware and are used in medical image analysis research and commercial products throughout the world.

  

This is a visualization of microvasculature captured by acoustic angiography. Computer-aided diagnostic analysis of vessels near tumors can distinguish benign from malignant tumors. The vascular models and visualization are provided by Kitware. Data is courtesy of Sarah Shelton and Dr. Paul Dayton at UNC.

In addition to participating in the collaborative research effort, Kitware provides consulting services to groups that seek to build commercial systems using ITK and 3D Slicer, as well as Kitware's expertise in low-cost ultrasound applications, vessel quantification, and other medical technologies.

Research reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under Award Number R43CA165621. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Kitware Offers Training Course on Reconstruction Toolkit
Kitware announced a one-day training course that will cover the basics of the Reconstruction Toolkit (RTK) for both users and developers. The course will take place in Lyon, France, on November 18, 2015. RTK is an open-source and cross-platform software solution for fast circular cone-beam computed tomography (CT) reconstruction. It is based on the Insight Segmentation and Registration Toolkit (ITK).

The course will focus on understanding RTK's main features, discovering RTK software for each step of a cone-beam CT reconstruction, experimenting with RTK's command-line tools on simulated and real data, learning where to find elements of RTK's code, modifying an existing reconstruction filter, and writing a new application.
The course will be taught by Simon Rit from the CREATIS laboratory and the Léon Bérard Cancer Center, in addition to Cyril Mory from the Université Catholique de Louvain. Participants are asked to bring their laptops and should be familiar with the basics of ITK, CMake, C/C++, and cone-beam CT.

Early registration ends October 27, 2015. For more information on the course and how to register, please visit Kitware's training website at http://training.kitware.fr/browse/116. To learn about RTK, please go to http://www.openrtk.org/.

Kitware Welcomes New Team Members

Over the past several months, Kitware has witnessed significant growth in all of its United States locations (Clifton Park, NY; Carrboro, NC; and Santa Fe; NM), as well as in Lyon, France. Kitware is growing not only in size, but also in the development of software solutions. In particular, Kitware is delivering open-source computer vision technologies through the Kitware Image and Video Exploitation and Retrieval (KWIVER) toolkit; enhancing high-performance computing visualization and data processing through advances in parallel computing, simulation-workflow integration, and in situ analysis; expanding in data and analytics through participation in collaborative programs such as Defense Advanced Research Projects Agency (DARPA) Memex; and making an impact in the field of medical computing through technical expertise.

Kitware is pleased to welcome the following new team members, who joined in August and September.

John Hoare
John became a member of the Computer Vision team in Clifton Park, NY. John has over four years of experience developing research-focused robotics applications across multiple specialties including controls, planning, perception, and human-robot interaction. He received his B.S. in Computer Engineering from California Polytechnic State University and his M.S. in Computer Science from the University of Tennessee.

Sumedha Singla
Sumedha joined Kitware’s Carrboro, NC, office as a member of the Medical Computing team. Sumedha received her B.E. in Computer Science at Thapar University in Punjab, India. She then completed an M.S. in Computer Science at the University of Utah. Her research interests include machine learning, algorithms, software development, and analytics.

Lucas Gandel
Lucas joined Kitware in Carrboro as an intern on the Medical Computing team. He has knowledge of computer programming and image processing. Lucas received his B.S. in Applied Computer Science from École Supérieure de Chimie Physique Électronique de Lyon (CPE Lyon), where he is currently pursuing his M.Sc./M.Eng.

Clémentine Guicheteau
Clémentine joined Kitware as an intern in Lyon, France. She is pursuing a degree in engineering from the Université de Technologie de Compiègne. Clémentine is proficient in C, C++, Pascal, Cascading Style Sheets (CSS), HyperText Markup Language (HTML), and MySQL.

Thomas (TJ) Corona
TJ became a member of the Scientific Computing team in Kitware’s Clifton Park office. He received his B.S. in Physics and his B.A. in Russian Language and Culture with a minor in mathematics from Duke University. He went on to receive his M.S. in Physics from Massachusetts Institute of Technology and his Ph.D. in Physics and Astronomy from the University of North Carolina at Chapel Hill. TJ has extensive experience in constructing mathematical and physical models in C++ in a collaborative environment, as well as in developing high-performance computing software for distributed systems.

Hyun Jae Kang
Hyun Jae became a member of the Medical Computing team in Carrboro. He has extensive experience in programming, software design, and research and development for medical imaging and surgical navigation systems. Hyun Jae received his B.S. in Mechanical Engineering from Kyungpook National University, his M.S. in Mechanical Design and Production Engineering from Seoul National University, and his M.S.E. and Ph.D. from the department of computer science at Johns Hopkins University.

To meet all of the new additions to Kitware from the spring and summer, please read our blog on http://www.kitware.com/blog/home/post/935. Information on becoming part of Kitware through employment and internship opportunities is detailed below.

Employment Opportunities

Kitware is seeking talented, motivated, and creative individuals to fuel innovation, break down boundaries, and join in its mission to develop and deliver state-of-the-art software products and services. The impact of research at Kitware extends far beyond the organization, as Kitware's open-source business model allows its members to become part of the worldwide communities that surround Kitware's projects.

Kitware employees enjoy a collaborative work environment that empowers them to pursue new opportunities and to challenge the status quo through novel ideas. In addition to providing an excellent workplace, Kitware offers comprehensive benefits including flexible hours; a computer hardware budget; health, vision, dental, and life insurance; short- and long-term disability insurance; immigration and visa processing; a relocation bonus; tuition reimbursement; and a generous compensation plan.

For additional information, please visit Kitware's employment website at http://www.jobs.kitware.com. Interested applicants are encouraged to submit their resumes and cover letters through the online portal.

Kitware Internships

Kitware internships provide college students with the opportunity to gain training and hands-on experience working with leaders in their fields on cutting-edge problems. Interns assist in developing foundational research and technology across Kitware's five solution areas: high-performance computing and visualization, computer vision, medical computing, data and analytics, and quality software process.

To find out more, please visit Kitware's employment website, or reach out to Kitware team members at an upcoming event, such as the 15th Annual North Carolina Master's & PhD Career Fair, which will take place on November 17, 2015, from noon to 4 p.m.

Questions or comments are always welcome!