Free Open Source Software for IGT

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Free Open Source Software for IGT

• Ron Kikinis, M.D.
• Professor of Radiology,
• Harvard Medical School

Founding Director, Surgical Planning Laboratory,
Brigham and Womens Hospital Principal
Investigator, National Alliance for Medical Image
Computing (a National Center for Biomedical
Computing, part of the Roadmap Initiative), and
Neuroimage Analysis Center (a NCRR National
Resource Center) Research Director, Image Guided
Therapy Program, Brigham and Womens Hospital
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Acknowledgments

• F. Jolesz, W. Lorensen, W. Schroeder, C. Tempany,
  P. Black, K. Hynynen, S. Wells, N. Hata, S.
  Warfield, CF. Westin, M. Halle, S. Pieper, and
  many more.

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Types of IGT Research

• Testing of devices provided by commercial vendors
• Can be done in a clinical environment
• Modification of existing devices
• Requires dedicated research time
• New methods
• Requires dedicated research time and dedicated
  personnel

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The Two Worlds of IGT

• Clinical devices
• Government regulated (for protection)
• Freeze the procedure and devices
• Characterize behavior
• Document
• Research devices
• Regulated through research protocols
• Frequent modifications
• Characterization/testing is an afterthought
• Documentation is always behind

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IGT Today

• IGT has a history of proprietary approaches
• Hardware is by default proprietary
• Funding agencies often require commercialization
  which is easier with proprietary approaches

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Consequences

• Proprietary software and hardware
• Locks researchers to a single vendor
• Prevents leveraging of the work of other
  scientists
• Graduate students (the work force of science)
  eternally reinvent the wheel

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NA-MIC A Template ?

• National Alliance for Medical Image Computing
• Academic and commercial partners
• Funded by NIH
• Leverages other work at the participating sites

Provided by Kikinis
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What is NA-MICs science?

• Computational tools for image analysis
  (algorithms)
• Software engineering methods and applications for
  image analysis (tools)
• Application science

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A Public Highway

• NA-MIC kit is like a Public Road System
• Provides open source infrastructure
• Driveways can Lead to Anything
• a Private Facility (commercial product)
• a Public Park (FOSS)
• FOSS Free Open Source Software

Provided by Pieper, Kikinis
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BSD style what does that mean?

• Open Source No restrictions on use
• No license fees
• You can use the source code to develop a
  commercial package that you sell. No need to ask
  for permission.
• If you use our software, you are responsible to
  make sure that you comply with all regulations
  that apply to the way you use it.
• E.g. if you want to use it for clinical trials,
  you have to apply for the proper authorizations
  at your institution
• You MUST acknowledge our contribution
• E.g. Insert a text like the following into the
  about section of your package or product This
  product is based on the 3D slicer software, see
  www.slicer.org for more information
• You can contribute back to us. It is your choice,
  if you want to do that and it is our decision, if
  we will accept it.
• BSDBerkley Software Distribution

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The NA-MIC Kit

• 3D Slicer Plattform for delivering image
  analysis technology to end-users
• Several toolkits, other infrastructure, and
  methodologies
• Native support for several plattforms Windows,
  Linux, OS X, Solaris

Provided by Pieper, Kikinis
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3D Slicer

• Application for image analysis and data
  visualization
• Free Open Source Software available for Windows,
  Linux, Solaris and Mac OS X
• Supports a large number of image formats
• Google slicer 101 for more information

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Segmentation
Provided by K. Pohl
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Rigid Registration
Provided by Talos, Pieper et al.
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Analysis of Tubular Structures

• Diffusion Tensor Imaging
• Automatic extraction of anatomically meaningful
  fiber bundles in the WM of the brain
• Cluster Analysis
• Rendering outside Slicer using photon mapping

Provided by Banks, Shenton, Kindleman, Westin,
Bouix, et al.
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Tracking
E.g. MicroBird Sensor fits on tip of flexible
scopes
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Development Methodology
Testing
CMake CTest CPack
Dashboard
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Tools

• Suite of software engineering tools supporting a
  multi-site development effort
• Cmake multiplatform compilation using native
  compilers (windows, OS X, Linux, Solaris)
• CTest automatic testing after compilations
• Dart2 web-based management of the development
• CPack Platform sensitive automatic installation
  of software

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CMake

• Manage the build process
• Find system libraries and code
• Compile source code
• Assemble resulting binary modules
• Create libraries
• Construct executables
• Enable customization, e.g.
• Specify location of source, object code,
  executables
• Build debug or optimized
• Do it cross-platform, combinations of
• hardware
• software
• compiler
• compiler options
• Do it fast
• Parallel compilation
• Rapid dependency checking

CMake is like a universal remote that
controls multiple build environments with a
single interface. CMake manages complex
software development environments like a
universal remote control automatically manages
the components of a multimedia system by simply
specifying the media type
Provided by Schroeder, Cedilnik
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Adoption Beyond Medical
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NCIGT

• National Center for Image Guided Therapy
• NIH funded
• Leverages NA-MIC software platform

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IGT Specific Capabilities

• Open Standards are needed for
• Trackers
• Scanner control
• Navigation systems
• Robotic devices

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Hardware Standards

• USB keys are an excellent example for a
  successful hardware/software standard
• Devices available from different vendors
• Same device works on different computers with a
  variety of operating systems
• Closer to IGT Opentracker is an emerging BSD
  licensed package that provides an open interface
  to several proprietary tracking systems

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Recommendations

• Free Open Source Software
• NA-MIC methodology allows multi-party development
  and quality assurance
• Potential to bridge the gap between research and
  clinical devices
• Open Standards for Hardware interfaces
• Computer industry offers good templates
  Standardization through ACM and IEEE

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Commercial Efforts

• Commercialization is the proper channel for
  distributing clinical devices
• Value-added commercialization is the proper
  mechanism to take advantage of open research
• The proposed framework with BSD style license and
  infrastructure for automated testing lowers the
  threshold for translational work

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IGT Engineering Workshop ncigt.org
Date October 19-20, 2006. Location Rockville,
MD Open to everybody Attendance limited by
size of venue only
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For More Information

• National Center for Image Guided Therapy
  www.ncigt.org
• Surgical Planning Laboratory www.spl.harvard.edu
• National Alliance for Medical Image Computing
  www.na-mic.org