Open Source Imaging Toolkits Rick Avila Director of

Open Source Imaging Toolkits Rick Avila Director of Medical Applications Kitware, Inc. rick. avila@kitware. com April 27, 2006 Kitware

The Software Gap Digital healthcare networks are rolling out across the planet… CT Lung Scan Slice Thickness Digital acquisition devices are exceeding observer ability… Comprehensive disease management tools are needed within a PACS workflow… Brain Lung Cardiac Colon Kitware

Improving Global Development Efficiency Baseline Data Publication Open Science 1. Open Data Env/Algs/ Apps Years Clinical Study Data Validation/ Analysis 2. Open Source 3. Open Publication Closed systems yield slow advancement Need rapid acquire / develop / validate / review cycles Kitware

Leveraging Global Resources Experts Development Tools • Clinical • Computing • Build Utilities • Quality Dashboard Imaging Toolkits Computing Resources • Software Architecture • Algorithms • Documentation • Validation Tests • Hardware & Software Datasets • All Diseases/Modalities Kitware

Open Source Imaging Toolkits Visualization Toolkit (VTK) Insight Toolkit (ITK) Rendering and Display Image Analysis High Quality, State-of-the-art Toolkits for Research and Product Development Kitware

The Visualization Toolkit (www. vtk. org) – C++ class library for visualization – Designed using object-oriented principles – Portable across Unix, Linux, Windows, Mac. OSX – Automated Java, TCL, Python bindings – Automated nightly testing – Supports 3 D/2 D graphics, visualization, image processing, and volume rendering – BSD-style license Kitware

VTK Kitware

VTK by the Numbers Community 65 2655 VTK C++ Files core developerson mailing list Source Code 1, 298 C++ classes 737, 359 lines of C++ code Daily Testing Snapshot 72 74 897 machine configurations (hw + sw) build and test sessions/day regression tests/build Kitware

Volume Rendering (Out Scattering) t’ t 0 (Absorption) t t 8 w’ w (In Scattering) (Emission) t 8 t Q(t) e I(t 0, w) = - sa(t’) + ssc(t’)dt’ t’ = t 0 dt (1) t = t 0 Q(t) = q(t) + rsc( w’ w) I(t, w’) d w’ 4 p (2) Kitware

Volume Rendering Architecture Property. . . Renderer Prop Collection Volume Image Data Volume Ray. Cast Function Volume Mapper Input Volume Property Mapper Volume Ray. Cast Mapper Gradient Estimator Gradient Shader Gradient Encoder Kitware

Volume Rendering Methods 1) Ray Casting • Floating Point • Composite w/shade • Gradient Magnitude Opacity • MIP • Iso. Surface • Fixed Point 2) Shear Warp 3) Texture Mapping • 2 D • 3 D 4) Volume. Pro Hardware (past) …with support for LOD control, multi-threading, … Kitware

VTK Dashboard using DART Kitware

CMake (www. cmake. org) Recently Adopted By Linux KDE Kitware

ITK: The Insight Toolkit (www. itk. org) $13 M directly invested to date • Toolkit started in 2000 • Open source segmentation & registration algorithms Kitware

ITK Developers Kitware

ITK • Image Processing • Segmentation • Registration • No Graphical User Interface (GUI) • No Visualization Kitware

ITK by the Numbers Community 58 1138 core developerson mailing list Source Code 1175 C++ classes 458, 770 lines of C++ code Daily Testing Snapshot 84 107 1195 machine configurations (hw + sw) build and test sessions/day regression tests/build Kitware

Registration in ITK Multi Resolution Registration Framework Image Registration Framework Registration Method Fixed Image Metric Components Optimizer Interpolator PDE Based Registration FEM Based Registration Fixed Image Moving Image Transform Registered Moving Image Kitware

Insight Journal PDF doc Journal Repository Code Author Input Data Results Data Web Site Build Machines Kitware

Use of VTK / ITK • Research – – – Algorithm Development & Comparison Prototypes Higher-Level Application Toolkits • Products – – – Scanners Analysis Workstations PACS Interventional Devices Research Interfaces Kitware

Open Source Impact Hans Johnson Lab, University of Iowa – Lab uses ITK and VTK – Student working on atlas based segmentation method – Danielsson signed distance filter is a bottleneck Insight Journal 2/20/2006 – 9: 26 am: IJ mail arrives about EDT filter (PAMI ‘ 03) – 12: 30 am: Print and read documentation – 1: 00 pm: Embed and run EDT code – 1: 03 pm: !#%? ! It runs in only 3 minutes? (10 x) – 1: 10 pm: Compare results & do dance of joy – 4: 00 pm: Submit Insight Journal review Kitware

NAMIC: SLICER Kitware

Mac: OSIRIX Over 8000 Users ~250 Downloads/Day Kitware

Brain. Lab Vector Vision Link Provides a direct interface with the Vector. Vision IGS navigation system to design and implement new features and functionality Kitware

Product Use: Me. Vis. Lab Kitware

Vol. View Clinical (Work in Progress) Not FDA Approved for Clinical Use Kitware

Open Source Toolkit Growth 7, 359, 000 hits/month on public. kitware. com Kitware

Summary Open Source Imaging Toolkits – Efficiently leverage global skills and resources – Represents a large and growing resource – Accelerates healthcare research and product development – Will drive down the cost of healthcare Kitware

Thank You Kitware

Doxygen Manual Pages Kitware

Insight Software Consortium (ISC) A non-profit that provides open-science environments for developers and users involved in medical image analysis research Users’ and Developers’ Point of View Does the software work? Time and interaction to download and install? Documentation online and available for download? Consistent code quality? Active support for individual packages, e. g. , email lists? How can I learn more about the software? How can I contribute my research and data Open-source changes too quickly! What open-science sites are available? ISC Provides Dashboards Packaging Documentation Standard Coding Standard Support Standard ISC hosts tutorials: SPIE… The Insight Journal Backward compatible policy The ISC website, The IJ Kitware

Workshop Response • 37 Submissions • 90 Reviews • by 31 Reviewers • 261 Registered Users • Anonymous reviews allowed, but none were submitted • Reviewers scored – Sensitivity – Helpfulness Kitware

Open Data: NIH RIDER Database Kitware

vtk. Volume. Mapper Code is Continuously Explored and Tested by a Large Number of Users and Experts Kitware

Image Guided Surgery Toolkit Kitware

Kitware