SOURCES SOUGHT
99 -- ITK Algorithms, Extensibility, Integration, & Outreach for SimpleITK 2015
- Notice Date
- 8/11/2015
- Notice Type
- Sources Sought
- NAICS
- 611310
— Colleges, Universities, and Professional Schools
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Library of Medicine, 6707 Democracy Blvd., Suite 105, Bethesda, Maryland, 20894, United States
- ZIP Code
- 20894
- Solicitation Number
- NIHLM2015597KB
- Archive Date
- 9/1/2015
- Point of Contact
- Keturah D. Busey, Phone: 3014966546
- E-Mail Address
-
buseyk@mail.nlm.nih.gov
(buseyk@mail.nlm.nih.gov)
- Small Business Set-Aside
- N/A
- Description
- This Sources Sought Notice is for informational and planning purposes only and shall not be construed as a solicitation or as an obligation or commitment by the Government. This notice is intended strictly for market research. This is a Small Business Sources Sought Notice. This is NOT a solicitation for proposals, Quotation abstracts, or quotations. The purpose of this notice is to obtain information regarding: (1) the availability and capability of qualified small business sources; (2) whether they are small businesses; HUBZone small businesses; service- disabled, veteran-owned small businesses; 8(a) small businesses; veteran-owned small businesses; woman-owned small businesses; or small disadvantaged businesses; and (3) their size classification relative to the North American Industry Classification System (NAICS) code for the proposed acquisition. Your responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. An organization that is not considered a small business under the applicable NAICS code should not submit a response to this notice. BACKGROUND In 1999, the NLM Office of High Performance Computing and Communications awarded multiple contracts for the formation of a software development consortium to create and develop an application programmer interface (API) and first implementation of a segmentation and registration toolkit, subsequently named the Insight Toolkit (ITK). The original awards included six contractors: GE Global Research, Insightful, Inc., Kitware, Inc., the University of North Carolina at Chapel Hill, the University of Pennsylvania, and the University of Tennessee. The six contractors were partnered with five subcontractors: Harvard University Medical School, the University of Pennsylvania, the University of Pittsburgh, Columbia University, and the University of Utah. The period of performance for the original ITK awards began in 1999 and ended in 2003. The resulting system was originally intended for computer-assisted exploration of the National Library of Medicine (NLM) Visible Human (VHP) Male and Female data sets. The final deliverable for this group was an open-source software library concentrating on segmentation and registration algorithms, directly released to the public that now helps support research worldwide in image analysis and in other domains. In 2002 and later in 2004, NLM funded outreach efforts known as the program for "ITK Algorithms, Adapters, and Data Distribution" (ITK-A2D2). These programs promoted ITK, tested the ITK API, evaluated the coverage of the algorithm collection, and explored the versatility of the software architecture. In the past, twenty separate awards were made including funding for: Kitware, Inc. Ken Martin, P.I. Application of Segmentation and Registration Techniques to Volume Visualization Georgetown Univ., Kevin Cleary, P.I. Integrating ITK Segmentation Components into an Existing Software Application for RF Ablation Treatment Planning Mayo Clinic, Rich Robb, P.I. Interface for Direct and Seamless Use of ITK with Analyze and AVW Cognita, Corp., Dan Fritsch, P.I. Integrating the SNAP (Snake Automatic Partitioning) Segmentation Tool with the NLM Insight Toolkit Imperial College of London, Derek Hill, P.I. 2D-3D Registration Software for X-ray-to-CT Alignment to the Visible Human Insight Toolkit Univ. of Iowa, Vincent Magnotta, P.I. Images, Landmarks, and ROIs Univ. of Utah, Yarden Livnat, P.I. Software Design and Development for Integration of the Insight Toolkit and the SCIRun Problem Solving Environment Insightful, Inc., Lydia Ng, P.I. Shape-based Level Set Segmentation Univ. of Pittsburgh, George Stetten, P.I. Real Time 3D Echocardiographic Data with Semi-Automated Boundary Tracking Algorithms Harvard BWH Surgical Planning Laboratory, C.F. Westin, P.I. Vascular Segmentation Using Level Sets for Image Guided Therapy Kitware, Inc., W. Schroeder, P.I. 3D Widgets for Segmentation and Registration Univ. of Pennsylvania, Jim Gee, P.I. ITK Surface-based Analysis and Normalization Environment Univ. of Pennsylvania, Jim Gee, P.I. Graph-Based Methods of Energy Minimization in ITK Univ. of North Carolina at Chapel Hill, Stephen Aylward, P.I. Neural Networks and Clustering Univ. of North Carolina at Chapel Hill, Stephen Aylward, P.I. DICOM and Digital Libraries for Data Archiving Univ. of North Carolina at Chapel Hill, Stephen Aylward, P.I. BatchMake and Validation Dashboards Univ. of North Carolina at Chapel Hill, Stephen Aylward, P.I. Insight Software Consortium Georgetown Univ., Kevin Wong, P.I. ITK Implementation of Deformable Registration Methods for Time-Varying (4D) Imaging Data Georgetown Univ., Kevin Cleary, P.I. Tumor Volume Measurement and Volume Measurement Comparison Plug-in for ITK Kitware, Inc., Bill Hoffman P.I. The Insight Journal: an Open Access Repository for Technical Papers related to the Insight Toolkit (ITK) In 2010, with funding from the American Recovery and Reinvestment Act, NLM sponsored a revision and redesign effort, IKT-version4 (ITK-v4), along with an outreach program to test and evaluate the revised API (ITK-A2D2-2010). Part of the ITK-v4 effort was a project to ease the burden of the steep learning curve of ITK, resulting in SimpleITK, an interface that allows multiple language bindings. We recognize that on of the most aggressive communities in scientific computing today include groups that development and use the NumPy and SciPy libraries with the Python programming language. Python is developed under an OSI-approved open source license, making it an attractive outlet for ITK integration and extension efforts. Open-source initiatives such as ITK help to lower the barriers to entry in complex research fields by providing the foundations of the software infrastructure necessary to conduct advanced investigations. Expanding the use of ITK through SimpleITK to open-source-friendly communities such as Python programmers is considered a contribution to the nation's infrastructure through software. Careful thought has been placed on the cultivation and maintenance of this software, assuring developers that the software will remain supported with new releases, bug fixes, and continuing growth. PURPOSE and OBJECTIVES The National Library of Medicine (NLM) is seeking to improve the position of its software libraries with respect to modern scientific computing software development environments. NLM has established projects to provide multiple language bindings for its open-source image processing application programmers interface (API) for image analysis, known as the Insight Toolkit (ITK). Notably, NLM supports SimpleITK, a simplified layer on tope of ITK, intended to facilitate its use in rapid prototyping and education and easing the learning curve for ITK by providing access to the library of algorithms and methods through scripting languages that are considered more facile and easier to use by the beginning programmer. We have noted that in recent years, the Python programming language has risen in prominence and is now being used in instruction for entry-level programmers at college-level, high-school-level, and even middle-school-level computer science education. We propose a new outreach effort to help broaden the user community and raise the awareness and effectiveness of SimpleITK, and by association of ITK, through modest awards that will promote the addition of needed algorithms to ITK and SimpleITK, improvements in exposing data structures and buffers for sharing across programs, additional support for the building and installation of SimpleITK direct installation and use of SimpleITK with the Python interpreter or similar programming environment. The objective of this program is to update and modernize the use of ITK through SimpleITK by making our tools more accessible to a modern scientific programming community. The emphasis of this effort will be expanding the software framework, broadening application development efforts, and data sharing to promote open science. PROJECT REQUIREMENTS NLM is seeking proposals for: 1. programming that extends ITK through incorporating additional algorithm families not already represented in ITK or projects that incorporate ITK into software and hardware systems in support of clinical or medical research applications (with an emphasis on multidisciplinary, practical applications not yet covered by ITK such as microscopic image analysis, ultrasonography, video processing, and other topics). All work on these core algorithm developments should be executed in C++ in ITK, and the necessary JSON files and other metadata produced to generate the necessary language bindings for extended use through SimpleITK. AND/OR 2. programming to overhaul and upgrade some valuable or necessary existing applications, examples, or algorithm family within ITK with the express purpose of improving compile and performance testing, enabling streaming for large data, out-of-core computing, promoting thread safety and encouraging multithreaded programming, and leveraging ITK hardware acceleration techniques. All work improving such core algorithm developments should be executed in C++ in ITK, and the necessary JSON files and other metadata produced to generate the necessary language bindings for extended use through SimpleITK. AND/OR 3. extension of SimpleITK and ITK to other development environments, notably exposing data structures for easy access with NumPy/SciPy programming. Specifically, we are seeking integration improvements with the core scientific Python package NumPy by having the SimpleITK's Image class directly export the "buffer interface", while preserving the Image's controlled access patterns to enable copy-on-write behavior. Alternately or additionally, to facilitate importing data from Numpy and other generic "buffers", we would like more support for more complicated memory layouts which include strides should be explored for ITK's ImportImageContainer class. AND/OR 4. easing the use of SimpleITK with current scientific computing environments, namely Python-based NumPy/SciPy models, through automated CMake-supported building, installation and packaging of SimpleITK through Python's standard distutils' "setup" interface from the python setup script. This will enable Python users to use Python standards tools for package management such as pip with SimpleITK without directly using CMake. Additionally this should support automatic downloads and compilation of source code for installation directly from source code archives. AND/OR 5. demonstration of SimpleITK and ITK by assembling image analysis suites from available algorithmic building blocks, for example constructing a framework for atlas-based segmentation through existing SimpleITK/ITK tools in segmentation of individual datasets and SimpleITK registration of unknown datasets to known atlas models. AND/OR 6. planning and executing educational efforts to promote SimpleITK at conferences, professional societies, and within university curricula while building tutorials, examples, and teaching materials that can be incorporated into the SimpleITK web site and other portals for continuing outreach. Some example concepts for this work include: • Algorithms or families of methods not currently represented in ITK and without interface support through SimpleITK. • Multiscale genome to physiological expression segmentation and visualization with SimpleITK/ITK support. • Large data, out-of-core data processing applications including image analysis for microscopy • An image analysis framework for comparing algorithm performance which might include measure computer-aided diagnosis tools or biomarker evaluation through ROC analysis • ITK supportable software for creating PACS research archives with automatic scrubbing and de-identification of patient information across PACS vendors. • A demonstration of ITK algorithms and the use of SimpleITK with Python in the development of a multi-atlas for atlas-based segmentation of medical image data. • CMake programming and configuration to enable SimpleITK packaging and delivery through Python's distutils facility. • Integration with the core scientific Python package NumPy by having the SimpleITK's Image class directly export the "buffer interface", while preserving the Image's controlled access patterns to enable copy-on-write behavior. • Support for more complicated memory layouts which include strides should be explored for ITK's ImportImageContainer class to facilitate importing data from NumPy. • Support for pickling of SimpleITK objects including Images and Transforms. This will add support for standard Python serialization enabling other scientific Python tools such as IPython's Parallel module. ANTICIPATED PERIOD OF PERFORMANCE It is anticipated that the period of performance shall be between twelve (12) from the date of award. Awards are anticipated to be made in September of 2015. OTHER IMPORTANT CONSIDERATIONS The proposed acquisition will be procured in accordance with the policies and procedures under FAR 13-Simplified Acquisition Procedures and FAR Part 12- Commercial Items. All responsible sources may submit a capability statement which will be considered by the National Library of Medicine. This Sources Sought Notice is not a Request for Quotation (RFQ), nor is an RFQ available. Interested firms responding to this Sources Sought Notice must adhere to the following: (a) Provide a capability statement demonstrating relevant experience, skills and ability to fulfill the Government's requirements for the above. The capability statement should contain enough sufficient detail for the Government to make an informed decision regarding your capabilities; however, the statement should not exceed 10 pages. (b) The capability statement must identify the responder's: small business type and size; DUNS number; NAICS code; and technical and administrative points of contact, including names, titles, addresses, telephone and fax numbers, and e-mail addresses. (c) All capability statements must be submitted electronically no later than 12:00pm eastern standard time on August 17, 2015 to Keturah Busey, at buseyk@mail.nlm.nih.gov. Disclaimer and Important Notes: This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization's qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published in Federal Business Opportunities. However, responses to this notice will not be considered adequate responses to a solicitation. Confidentiality: No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s). Contracting Office Address: 6707 Democracy Blvd., Suite 105 Bethesda, Maryland 20894 United States Place of Performance: TBD United States Primary Point of Contact.: Keturah D. Busey, Contract Specialist buseyk@mail.nlm.nih.gov Phone: 3014966546
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