Free Open Source Software for IGT

Surgical Planning LaboratoryBrigham and Women’s HospitalBoston, Massachusetts USA

a teaching affiliate ofHarvard Medical School

Free Open Source Software for IGT

Ron Kikinis, M.D.

Professor of Radiology,

Harvard Medical School

Founding Director, Surgical Planning Laboratory, Brigham and Women’s HospitalPrincipal 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 Women’s Hospital

©2006 Surgical Planning Laboratory, ARR Slide 2

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….

V E R I TAS


Types of IGT Research

1. Testing of devices provided by commercial vendors

• Can be done in a clinical environment

2. Modification of existing devices• Requires dedicated research time

3. New methods• Requires dedicated research time

and dedicated personnel


The Two Worlds of IGT

• Clinical devices– Government regulated (for protection)

1. “Freeze” the procedure and devices

2. Characterize behavior

3. Document

• Research devices– Regulated through research protocols

1. Frequent modifications

2. Characterization/testing is an afterthought

3. Documentation is always behind


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


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


NA-MIC: A Template ?

Provided by Kikinis

• National Alliance for Medical Image Computing

• Academic and commercial partners

• Funded by NIH• Leverages other

work at the participating sites


What is NA-MICs science?

• Computational tools for image analysis (algorithms)

• Software engineering methods and applications for image analysis (tools)

• Application science


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


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.

• BSD=Berkley Software Distribution


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


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


Segmentation

Provided by K. Pohl


Rigid RegistrationOverlay Before:

After:

Provided by Talos, Pieper et al.


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.


Tracking

E.g. MicroBird Sensor fits on tip of flexible scopes


Development Methodology

6 months

4 months

2 months

Release Patch Nightly Continuous

Release X.Y

Release X.Y.1

Release X.Y.2

Release X.Y.3

Extreme lifecycle

Dashboard

CMakeCTestCPack

Testing

PrivateSandbox

NA-MICSandbox

Slicer

ITK

Prototype


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


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 controlsmultiple 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


Adoption Beyond Medical


NCIGT

• National Center for Image Guided Therapy

• NIH funded

• Leverages NA-MIC software platform


IGT Specific Capabilities

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


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


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


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


IGT Engineering Workshop: ncigt.org

Date: October 19-20, 2006.

Location: Rockville, MD

Open to

everybody

Attendance limited by size of venue only


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

Documents

Free Open Source Software for IGT