Kitware News

Best Industry-Related Paper Won by Kitware at ICPR 2014

The IEEE/IAPR International Conference on Pattern Recognition (ICPR) is the premier international conference for the latest academic and industry research in pattern recognition on images, video, biomedical data, and other domains. ICPR 2014, the 22nd in the biennial series, was held from August 24 to August 28, 2014, in Stockholm, Sweden. The conference featured 792 papers, four of which were selected as finalists for Best Industry-Related Paper. Industry-related papers were identified by track chairs as those pertaining to an application, system, or industry problem and included papers authored solely by academic institutions, as well as by industry authors. Kitware's winning paper, co-authored by Sangmin Oh, Megha Pandey, Ilseo Kim, Anthony Hoogs, and Jeff Baumes, is titled "Personalized Economy of Images in Social Forms: An Analysis on Supply, Consumption,
and Saliency."

Anthony Hoogs and one author from each of the other three finalists discussed the challenges and issues of conducting research in an industry setting during a plenary session panel discussion on August 26, 2014. The winner of the highly-selective award was announced following the discussion.

Kitware is developing a suite of large-scale multimedia analysis tools to advance visual content understanding, content-based search, online privacy protection, and network modeling. As detailed in the paper, these tools incorporate the latest techniques in multimedia analysis to detect objects, scenes, activities, in-scene text, and audio signals embedded in unconstrained images and videos. Patterns in behavior were detected with respect to images on Reddit.com through a unique approach based on two behavioral modes: "supply" and "consumption." Supply is defined as posting multimedia content, and consumption includes commenting on or interacting with previously posted multimedia content. Users were characterized based on the types of images they consumed and supplied.

The results of this research offer new findings to the field of social multimedia analysis. For one, it was observed that the types of images that many users supplied differed from those they consumed. This challenges the previously held notion that users are likely to post and comment on similar images. The paper also shows how to quantify and track the content-based behavior of users over time, revealing changes in their patterns. In addition, a significant proportion (15%) of users supplied more images than they consumed.

Award Received to Develop Retinal Image Management System (RIMS)

Kitware recently announced a $150,000 Department of Defense  Small Business Innovation Research (SBIR) Phase I award for the development of a Retinal Image Management System (RIMS).

Retinal damage is a debilitating condition, which, if left untreated, can lead to blindness. Retinal damage is widespread and has many causes, ranging from accidental exposure to environmental dangers to complications of disease such as diabetes (diabetic retinopathy).

While current retinal imaging tools that utilize a single retinal image to detect damage provide basic functionality for the investigation of ocular pathophysiology, more detailed information can be derived from using multiple imaging modalities. Furthermore, the tools typically used in today's research and clinical practice do not allow for comparative, simultaneous visualization and analysis of the damaged area. This places the burden on the researcher or clinician to mentally merge information from disparate sources. RIMS is designed to ease this burden by providing a single image presentation that fuses all available imaging data, and by linking to other metadata such as visual acuity test results.

RIMS will provide significant improvement in the study of physiological functional changes of the retina resulting from light induced damage, as well as the next generation retinal pathology system for general ophthalmic medical practice. Furthermore, RIMS will simplify patient education and boost patient awareness by relating patient history and providing easy-to-understand visualizations.

For the project, "Multimodal-Multidimensional image fusion for morphological and functional evaluation of the retina," Kitware will collaborate with DualAlign LLC, a recognized expert in ocular registration. Dr. Wesley Turner, a Technical Leader at Kitware, will serve as the Principal Investigator, and Dr. Chuck Stewart will lead the effort at DualAlign.

The goal of the Phase I effort is to design a system for the registration and analysis of multi-modality retinal images, and to create a Software Development Plan (SDP), which identifies I/O formats associated with 2D and 3D imaging modalities and complementary visual function tests; delineates desirable preprocessing capabilities for noise reduction in native images; details technical approaches for image registration and data fusion; defines the graphical user interface for data management; and outlines verification procedures.

This material is based upon work supported by the United States Air Force under Contract No. FA8650-14-M-6558. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the United States Air Force.

A montage of retinal thickness over a wide field obtained from the Zeiss Cirrus OCT and i2k Retina. Contributed by Joe Carroll, Wisconsin College of Medicine.

Windows Support for CMake Announced by Microsoft

In a Windows Blog post by Adam Denning, Microsoft recently announced Windows support for CMake. Microsoft’s fork of CMake, CMakeMS, provides developers with the ability to target Windows Store and Windows Phone apps. It is available on CodePlex. According the blog Microsoft plans to “incorporate feedback and integrate it soon in the public CMake repository” in collaboration with the CMake community and Kitware.

Medical Advances Highlighted at MICCAI

Kitware exhibited recent work in medical computing at the Medical Image Computing and Computer Assisted Intervention (MICCAI) 2014 conference in Boston, MA.

MICCAI 2014 is one of the premier conferences in the medical computing field, highlighting topics such as medical image computing, computer-assisted intervention, visualization, computer-aided diagnosis, and new imaging applications. Kitware actively participated in MICCAI 2014 and in the 7th Annual Image-Guided Therapy workshop, which was held in conjunction with the conference.

Kitware's involvement spanned presentations, tutorials, and panel participation. Collaborative research with the University of North Carolina on atlas-based segmentation and atlas building was presented in the paper "Low-Rank to the Rescue – Atlas-based Analyses in the Presence of Pathologies," which was co-authored Xiaoxiao Liu, Marc Niethammer, Roland Kwitt, Matthew McCormick, and Stephen Aylward.

Stephen Aylward, Kitware's Senior Director of Medical Research, served as an invited speaker for the "Building image-guidance systems from open-source components" tutorial. The hands-on tutorial showcased best practices in prototyping image-guidance systems for minimally invasive interventions using open-source software tools. In particular, the tutorial highlighted 3D Slicer.  

At Kitware, Dr. Aylward directs several research projects that focus on 3D Slicer, including the use of 3D Slicer to perform surface model registrations, which is demonstrated in the recently released video, "Fusing Surface Models and Medical Images, using the Structure Sensor and 3D Slicer."

Furthermore, as an advocate for scientists pursuing influential research in medical computing, Kitware once again sponsored the Young Scientist Publication Impact Award. This award, now in its fourth year, recognizes researchers who are making impactful progress on the field of medical image analysis while early in their careers.

Meanwhile, during the 7th Annual Image-Guided Therapy workshop, Ricardo Ortiz presented work on "Finite element based biomechanical analysis of cranial shapes for craniosynostosis surgical correction," which he co-authored with Andy Bauer, Andinet Enquobahrie, Nabile Safdar, Gary Rogers, and Marius Linguraru. The goal of this work is to shift the surgical correction procedure for pediatric patients with craniosynostosis from subjective visual assessments to a virtual surgery system for optimal treatment planning.

Framework Being Developed for Image Guidance for Orthognathic Surgery

Kitware is developing real-time image guidance to help address pressing challenges in the orthognathic surgical community. Orthognathic surgery is used to treat severe craniofacial anomalies and dentofacial deformities such as cleft lip and palate, under bites, open-bites, and sleep apnea. It involves the surgical repositioning of the facial skeleton to restore the proper anatomic and functional relationship of the jaws. If left uncorrected, misalignment of the jaws can lead to psychological distress, as well as impaired masticatory, speech, and respiratory functions, which can affect a person's overall quality of life.

While current 3D computer aided surgical simulation and 3D surgical splint modeling tools can help improve surgical outcomes for craniofacial deformities, they do not address the issue of surgical relapse. In addition, although they allow surgeons to visualize the positions of instruments relative to an immobile jaw, these tools do not offer real-time visualization of a movable jaw. In order to address these issues, Kitware is  developing a more advanced visualization technique is necessary.

The team will develop an intra-operative visualization technique that incorporates freehand ultrasound imaging technology and 3-D image registration techniques to assist oral maxillofacial surgeons as part of a Phase I Small Business Innovation Research (SBIR) project funded by the National Institute Of Dental and Craniofacial Research.

For this project, Kitware is collaborating with Dr. Tung Nguyen, Director of the Dentofacial Deformities Clinic, and Dr. Beatriz Paniagua, Research Assistant professor at the University of North Carolina School of Dentistry.  The team will begin by creating algorithms for orthognathic surgery planning, navigation, and visualization. These algorithms will be integrated into the 3D Slicer (Slicer) framework to create a prototype navigation system. The team will then evaluate the effectiveness, feasibility, and reproducibility of the protocol in simulated operating room conditions.

The project will leverage and extend best-of-breed tools including Slicer, which incorporates the Visualization Toolkit (VTK) in its infrastructure. Slicer is an open-source cross-platform toolkit for medical image processing and analysis that supports applications such as tractography, endoscopy, tumor volume estimation, and image-guided surgery. Slicer is in active use by the biomedical imaging research community as a vehicle to translate innovative algorithms into clinical research applications. As an engineering core member of the National Alliance for Medical Image Computing (NA-MIC), Kitware has been instrumental in developing new technologies for Slicer.

Research reported in this publication was supported by the National Institute Of Dental & Craniofacial Research of the National Institutes of Health under Award Number R43DE024334. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Promising Social Multimedia Breakthroughs Addressed at Workshop

The Science of Multi-INT (SOMI) Workshop brought together hundreds of technologists and government program managers interested in the fusion and exploration of sensor and data. Dr. Anthony Hoogs gave a presentation at the workshop entitled "Concept for Fusing Social Multimedia with Overhead Sensing for Situational Awareness in Denied Areas." Social media has become a rich source of intelligence as it is readily available in many denied areas, widely used, and nearly instantaneous. Overhead sensing and social media are highly complementary, and fusing them would enable the corroboration or refutation of information about the same person, event, or place, or lead to new insights that would not be possible from either on its own. Promising breakthroughs in automated visual content extraction from social multimedia were described, with a framework for fusing them with NTM content to solve hard A2AD problems.

Briefing Delivered at MSS Specialty Group Symposium

Kitware participated in this year's 2014 Meeting of the Military Sensing Symposium (MSS) Specialty Group on Active E-O Systems, which was held from August 26 to August 28, 2014, in Springfield, VA.  The focus of the symposium was on active Electro-Optical (EO) and Infrared (IR) systems for military, intelligence, and civil applications. It was held in tandem with the MSS Electro-Optical and Infrared Countermeasures Specialty Group and provided technical and strategic information to the combined community through presentations and detailed discussions.  

Rusty Blue, a Technical Leader on the Computer Vision team at Kitware, presented a brief on "Fusing 3D Point Data and Video for GPS-Denied Navigation" in the "Active Systems for Surveillance and Reconnaissance" session on August 27, 2014. During the presentation, he addressed some of the work in which Kitware has been participating that has the potential, when combined, to aid the soldier on the ground in a GPS-Denied environment. Such work includes Google Project Tango, for which Kitware is a partner.

Ice Bucket Challenge Website Created

Kitware announced the development of an open-source website that depicts a network of participants in the popular Ice Bucket Challenge, which has raised funds for The ALS Association. The website is located at http://infovis.kitware.com/ice-bucket/.

Members of Kitware’s Scientific Computing team found that despite the unending stream of news reports of celebrities performing the ALS Ice Bucket Challenge, no one report captures the true scale and proliferation of the challenge or highlighted the interesting connections between the participants.

Accordingly, Kitware created a simple open-source website on the Ice Bucket Challenge to show the breadth of participation in the fundraiser. The information visualization (InfoVis) on the website also addresses how and why particular people became involved in the challenge by linking participants to those who challenged them, as well as to those who they, in turn, challenged.

For the website, a simple data format was developed that is read by the site to list the participants in a grid, show details and related individuals, and link to posted videos of participants taking the challenge.

To further promote community involvement, Kitware is encouraging additions and corrections to the website from anyone who would like to participate. Those who would like to add or propose corrections to the website can submit information through the issues page. For the developer-inclined, Kitware urges others to fork its repository on GitHub and submit pull requests with additions to its JSON data file and image thumbnails.

CMake.org Website Redesigned

Kitware announced the rollout of the new cmake.org website. The new website design is intended to more easily provide dynamic and up-to-date content to the community, be mobile-friendly, and make information on how to use CMake more accessible. The website includes a "Get Involved" section, where the community can learn how to contribute to the open-source toolkit; resources and developer resources menus; and a quick access download button on the main page. CMake follows ParaView, Tangelo, and Open Chemistry in the transition of Kitware's open-source solutions websites to the new design.

Geodesic Regression Paper Presented at ECCV 2014

The paper "Geodesic Regression on the Grassmannian," which was written as part of a collaboration between Kitware; the University of North Carolina, Chapel Hill; the University of Salzburg; and the University of California, San Diego, was accepted for presentation at the European Conference on Computer Vision (ECCV) 2014. ECCV is one of the leading conferences for computer vision research. It was held from September 6 to September 12, 2014, in Zürich, Switzerland.

The paper was co-authored by Yi Hong, Roland Kwitt, Nikhil Singh, Brad Davis, Nuno Vasconcelos, and Marc Niethammer. It details a theory for Grassmanian geodesic regression (GGR) that extends linear regression to the Grassmannian. This work addresses the challenge of regressing data points on the Grassmann manifold over a scalar-valued variable. In addition, GGR offers a compact representation of the complete geodesic path and brings to light the possibility of statistical analysis on Grassmannian geodesics.

This research was tested on several vision challenges to demonstrate its applicability, namely the prediction of traffic speed and crowd counts from dynamical system models of surveillance videos and the modeling of aging trends in human brain structures using an affine-invariant shape
representation.

New Employees

Shawn Waldon
Shawn joined Kitware's Clifton Park, NY office as an R&D Engineer on the Scientific Computing team. He earned his B.S. in Computer Science and Mathematics from Appalachian State University and his M.S. in Computer Science from the University of North Carolina at Chapel Hill (UNC). Prior to joining Kitware, Shawn was a Research Assistant in UNC's Computer Science department.

Betsy McPhail
Betsy joined the Kitware team at the Clifton Park, NY office as an R&D Engineer on the Software team. Betsy received a B.S. in Computer Engineering with a minor in mathematics from Union College and an M.Eng. in Computer and Systems Engineering from Rensselaer Polytechnic Institute. Prior to joining Kitware, Betsy was a Software Engineer at Vistec Lithography, Inc.

David Manthey
David joined the Kitware team at the Clifton Park, NY, office as an R&D engineer on the Scientific Computing team. David received a B.S. in Mechanical Engineering from Rensselaer Polytechnic Institute. Prior to joining Kitware, he was a Senior Programmer for ReQuest Serious Play, LLC; a Programmer/Product Designer/Electronics Technician for Hitchcock-Manthey, LLC; and a Head Programmer/Product Designer for CamSys, Inc.

Deepak Chittajallu
Deepak joined the Kitware team at the Carrboro, NC, office as an R&D engineer on the Medical Computing team. Deepak received a B.Tech. in Computer Science and Information Technology from Jawaharlal Nehru Technological University, as well as an M.S. and a Ph.D. in Computer Science from the University of Houston. Prior to joining Kitware, he was a Postdoctoral Research Fellow at Harvard's Laboratory of Computational Cell Biology.

Upcoming Events and Courses

IEEE Nuclear Science Symposium & Medical Imaging Conference
November 8 to November 15, 2014 in Seattle, WA

Matt McCormick will teach a scientific Python course. The one-hour course will introduce and refresh participants regarding Pythonic practices from the perspective of a researcher with a C or C++ background. The topics that will be covered in the course include creating a reproducible computational environment with Docker; learning about interactive analysis and literate programming with the IPython shell and the IPython Notebook; surveying the fundamental scientific Python packages numpy, matplotlib, scipy, sympy, and pandas; writing efficient, compiled C/Python hybrid code with Cython; and wrapping C and C++ libraries in Python with XDress. This is a hands-on course that requires a laptop and active participation!

Supercomputing 2014
November 16 to November 21, 2014 in New Orleans, LA

SC14 is a premier conference in the scientific computing field. Kitware's participation in SC14 includes exhibiting a ParaView Showcase at its booth (#1354), presenting tutorials on Large Scale Visualization with ParaView and In Situ Data Analysis and Visualization with ParaView Catalyst, presenting a paper on extreme scale in situ visualization and analysis, taking part in the SC14 Student Job/Opportunity Fair, and authoring a paper on sustainable software ecosystems for the second Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2).

Advanced VTK Course
November 17, 2014 in Lyon, France

This advanced training is tailored to people who have a basic knowledge of VTK but want to extend their expertise. The training mixes theory and application with a set of tutorials and exercises. Through the course, attendees will learn parallel processing using VTK, how to use composite and temporal data, and how to develop new filters and readers. Prerequisites for the course include a basic understanding of the VTK library and knowledge of C++.

Advanced ParaView Course
November 18, 201 in Lyon, France

This training course is tailored for ParaView users and VTK developers who have a knowledge of the VTK library and who want to grasp ParaView deployment and initiate extension development.

Advanced Image Processing with ITK
November 19, 2014 in Lyon, France

This course will cover the basic features of ITK, from its design to the integration of an ITK alogirthm in an application. The course is geared toward R&D engineers and researchers in the image processing field. Objectives of this course include understanding the basic functions of ITK, learning how to create and run registration filters, understanding how to create an application using ITK, and learning how to create and run segmentation filters.

Computer Vision with OpenCV
November 20, 2014 in Lyon, France

This course will cover the main features of OpenCV, an open-source library dedicated to computer vision, through its core functionalities and advanced image processing modules. The training mixes theory and application with a set of tutorials and exercises. The objectives of the course include learning how to implement your own image processing algorithm, understanding the main structuries for image processing, and learning the possibilities of using OpenCV in computer vision applications.

Employment Opportunities

Kitware is seeking talented, motivated, and creative individuals to fill open positions. As one of the fastest growing companies in the country, Kitware has an immediate need for software developers and researchers. In particular, we are looking for scientific visualization developers who have C++ and JavaScript skills, as well as web development skills.

In addition, Kitware internships provide current college students with the opportunity to gain hands-on experience working with leaders in their fields on cutting-edge problems. We offer our interns a challenging work environment and the opportunity to attend advanced software training.

For more details, please visit our employment site at jobs.kitware.com. Interested applicants are encouraged to submit their resumes and cover letters through our online portal.

Questions or comments are always welcome!