2012 Progress Report IMPACT
5. IMPACT AND VALUE TO BIOCOMPUTING NA-MIC impacts the field of biocomputing through a variety of mechanisms. First, NA- MIC produces scientific results, methodologies, workflows, algorithms, imaging platforms, and software engineering tools and paradigms in an open environment that contributes directly to the body of knowledge available to the field. Second, NA-MIC science and technology enables the entire medical imaging community to build on NA- MIC results, methods, and techniques, to concentrate on the new science instead of developing supporting infrastructure, to leverage NA-MIC scientists and engineers to adapt NA-MIC technology to new problem domains, and to leverage NA-MIC infrastructure to distribute its own technology to a larger community.
5.1 Impact within the Center Within the center, NA-MIC has formed a community around its software engineering tools, imaging platforms, algorithms, and clinical workflows. The NA-MIC calendar includes the All Hands Meeting and Winter Project Week, the Spring Algorithm Meeting, the Summer Project Week, 3D Slicer Mini-Retreats, Core Site Visits, and weekly telephone conferences. These events bring the NA-MIC community and the community at large together to address emerging needs through the joint development and application of methods and systems.
The NA-MIC software engineering tools (CMake, CDash, CTest, CPack) have enabled the development and distribution of a cross-platform, nightly tested, end-user application, the 3D Slicer, that is a complex union of novel application code, visualization tools (VTK), imaging libraries (ITK, TEEM), data management (DCMTK), user interface libraries (Qt), and scripting languages (Python). The NA-MIC software engineering tools have been essential to the development and distribution of the 3D Slicer imaging platform to the NA- MIC community.
NA-MIC's end-user application, the 3D Slicer, supports the research within NA-MIC by providing a base application for visualization, image analysis, and data management. This reporting period marked the introduction of Version 4 of the 3D Slicer which provides a new underlying architecture and a modern user interface using Qt. The 3D Slicer supports multiplanar reformat, oblique reformat, surface and volume rendering, comparison viewers, tracked cursors, and multiple image layer blending. The 3D Slicer can communicate with XNAT and DICOM databases to download data and upload results. The 3D Slicer provides a multi-layer plugin mechanism, which permits researchers to quickly and easily integrate and distribute their technology with the 3D Slicer. Plugins can be authored as separate executables, shared libraries, Python scripts, or as full first class 3D Slicer modules. These plugins can be distributed with the 3D Slicer or distributed on a site maintained by the researcher (e.g., on the Neuroimaging Informatics Tools and Resources Clearinghouse, www.nitrc.org). The 3D Slicer is available to all Center participants and the external community through its source code repository, official binary releases, and unofficial nightly binary snapshots. There are 8 training modules for the 3D Slicer Version 4.1, which educate 3D Slicer Users on basic image review, use of advanced modules, and integration of new technology into the 3D Slicer. Webinars are used to introduce the new versions of the 3D Slicer.
NA-MIC drives the development of platforms and algorithms through the needs and research of its DBPs. Each DBP has selected specific workflows and roadmaps as focal points for development, with a goal of providing the community with complete end-to-end solutions using NA-MIC tools. Each DBP is connected to a member of the Engineering core and a member of the Algorithm core to orchestrate the NA-MIC activities to support their DBP. The four current DBPs in NA-MIC focus on the personal and longitudinal aspects of pathology and disease. These DBPs are Atrial Fibrillation, Traumatic Brain Injury, Adaptive Radiation Therapy, and Huntington's Disease. For each roadmap project, the software tools, exemplar data, and a tutorial are provided to the community to allow others to reproduce the results and apply the workflows in their own research programs.
NA-MIC algorithms are designed and used to address specific needs of the DBPs. Multiple solution paths are explored and compared within NA-MIC, resulting in recommendations to the field. The NA-MIC algorithm groups have collaborated on a broad spectrum of methods for Structural Image Analysis, Diffusion Image Analysis, and Functional Image Analysis and orchestrated the solutions to the DBP workflows and roadmaps. These efforts have led to fundamental advancements in shape representation, shape analysis, groupwise registration, diffusion estimation, segmentation and quantification, functional estimation, distortion correction, and clustering. To support the current DBPs, the algorithms team is focusing on Statistical Models of Anatomy and Pathology, Geometric Correspondence, User Interactive Tools for Segmentation, and Longitudinal and Time-Series Analysis.
5.2 Impact within NIH-Funded Research Within NIH-funded research, NA-MIC is the National Center for Biomedical Computing (NCBC) collaborating center for eight other grants: PAR-05-063: R01EB005973 Automated FE Mesh Development, PAR-05-063: R01CA124377 An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors, PAR-07-249: R01EB006733 Development and Dissemination of Robust Brain MRI Measurement Tools, PAR-07-249: R01MH084795 The Microstructural Basis of Abnormal Connectivity in Autism, PAR-07-249: R01CA131718 NA-MIC Virtual Colonoscopy, PAR-07-249: R01EB008171 3D Shape Analysis for Computational Anatomy, PAR-07-249: R01AA016748 Measuring Alcohol and Stress Interaction with Structural and Perfusion MRI, and PAR-08-183: R21EB009900 Johns Hopkins Skull Stripping.
NA-MIC also collaborates or has collaborated with other NIH funded organizations, including: U24RR026057 Collaborative Tools Support Network for BIRN, U24RR025736 BIRN CC, U54GM072970 NCBC Stanford Simbios, U54EB005149-04S1 NA-MIC Collaboration with NITRC, COPDGene® quantitative analysis, R01NS050568 BRAINS Morphology and Image Analysis, NCBC Supplement for Microscopy and Slicer, R01CA111288 NA-MIC Collaboration with Prostate BRP, U24RR021992 fBIRN, U41RR019703 NA-MIC Collaboration with NCIGT, U54LM008748 NCBC I2B2, U24RR021382 mBIRN, P41RR013218 NA-MIC Collaboration with NAC, BrainColor, Real-Time Computing for Image Guided Neurosurgery, UL1RR025758 NA-MIC support for Harvard CTSC Translational Imaging Consortium, Children's Pediatric Cardiology Collaboration with SCI/SPL/Northeastern.
NA-MIC events and tools garner national and international interest. Over 100 researchers participated in the NA-MIC All Hands Meeting and Winter Project Week in January 2012. Attendees were from 19 academic sites and 6 companies. Many of these participants were outside of NA-MIC and were attending the meetings to gain access to the NA-MIC tools and researchers. The Winter Project Week was expanded to include NA-MIC, NAC, NCIGT, CIMIT, and Cancer Care Ontario.
5.3 National and International Impact NA-MIC collaborations include a number of international communities and organizations, including: Ontario Consortium of Adaptive Interventions for Radiation Oncology (OCAIRO), Computer Aided and Image Guidance Medical Interventions (CO-ME), NA-MIC Collaboration for Neurosurgical Intervention with University Hospital of Marburg Germany, Common Toolkit (CTK), Real Time Computer Simulation of Human Soft Organ Deformation for Computer Assisted Surgery, NA-MIC Collaboration with Research and Development Project on Intelligent Surgical Instruments, and the Vascular Modeling Toolkit Collaboration. NA-MIC collaborates with the organizations at all levels: tools, algorithms, clinical domain, and training.
Components of the NA-MIC kit are used globally. The software engineering tools of CMake, CDash, and CTest are used by many open-source projects and commercial applications. For example, the K Desktop Environment (KDE) for Linux and Unix workstations uses CMake and CTest. KDE is one of the largest open source projects in the world. Many open source projects and commercial products are benefiting from the NA-MIC related contributions to ITK and VTK. The 3D Slicer version 4 has been downloaded 16,375 times since its introduction in November 2011. The 3D Slicer also is being used as an image analysis platform in several fields outside of medical image analysis, in particular, biological image analysis, astronomy, and industrial inspection.
NA-MIC science is recognized by the medical imaging community. There are 332 NA-MIC related publications listed on PubMed. Many of these publications are represented in the most prestigious journals and conferences in the field. Overall, there are 516 publications that acknowledge NA-MIC support. Portions of the DBP workflows and roadmaps already are being used by researchers in the broader community and in the development of commercial products.
NA-MIC sponsored several events to promote NA-MIC tools and methodologies. In 2011 alone, NA-MIC hosted 12 workshops and training sessions at 11 domestic and international venues. Several of these workshops were held at international conferences including RSNA, SfN, AAPM, and MICCAI. The workshops and training sessions are individually targeted to meet the specific needs and interests of clinicians, biomedical engineers, or algorithm developers. Four hundred and fifty-seven clinical, biomedical, and algorithm researchers attended these events. Since 2005, two thousand and twelve clinical, biomedical, and algorithm researchers have been trained by NA-MIC. Aside from workshops and training events, NA-MIC had a physical presence at HBM and RSNA in the form of a booth. The booth at RSNA marked the introduction of 3D Slicer Version 4, was available for 54 hours of the conference, and provided attendees a selection of 13 hands-on demonstrations.