core 1b – engineering end-user platform

NA-MICNational Alliance for Medical Image Computing http://na-mic.org

Core 1b – Engineering

End-user Platform

Steve Pieper

Isomics, Inc.

National Alliance for Medical Image Computing http://na-mic.org

Topics

• 2011 Year in Review– 3D Slicer version 4.0

– Highlights

• Plans for This Week and Beyond


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Core 1b – Engineering5 Aims / 5 Platforms

Architecture – tools, operating paradigms, reporting mechanisms, integration points

End-user platform – interactive methods and information visualization for longitudinal analysis, exploratory data analysis, and translational research

Computational platform – stream processing, cloud computing, statistical analysis, informatics, machine learning

Data management – non-imaging and derived data, DICOM and cloud services

Software engineering and software quality – navigable timeline for revision control, build, test, documentation and release


End-user platform

• 3D Slicer: a cross platform system for translating innovative algorithms into clinical research applications

Developer NeedsClinical Grade IO and UI

Rich Utility Libraries

Extensible and Reconfigurable

Stable Base

Easily Deployable

Developer NeedsClinical Grade IO and UI

Rich Utility Libraries

Extensible and Reconfigurable

Stable Base

Easily Deployable

User NeedsEasy Install and Upgrade“Standard” Clinical BehaviorConsistent InterfaceAdvanced Functionality

User NeedsEasy Install and Upgrade“Standard” Clinical BehaviorConsistent InterfaceAdvanced Functionality


• Clinical Grade IO and UI• Slicer developers work closely with DBPs on real data and are

exposed to clinical state of the art

• Rich Utility Libraries• NA-MIC Kit

• Extensible and Reconfigurable• Loadable Extensions• Scriptable GUI

• Stable Base• Nightly Extensions Built Against Latest Slicer Release• Slicer Release Relies on Upstream Release (ITK, VTK, etc)

• Easily Deployable• Binary Installers for all platforms

Developer Needs


• Easy Install and Upgrade• Binary installers and Extension Wizard

• “Standard” Clinical Behavior• Adhere to Conventions where Possible

• Varies by Domain (IGT Navigation vs. Neuroscience Research vs. RT Planning)

• New Functionality has no “Standard” by Definition

• Consistent Interface• Learning one Slicer Module should help you know how to use

other ones

• Advanced Functionality• Main Motivation: you use slicer because nothing else does

what you need – we try to make that as painless as possible

User Needs


Our Solution: 3D Slicer

• Focus for NA-MIC DBPs and Collaborations• Platform and Reusable Parts for Wider Community


Impact – June 2008 – Dec. 2011

Slicer3 Download Statistics


We’ve been busy in 2011…

Cue the movie…


Results: For Users

• Faster– Startup

– Interaction

• More Stable• New Qt Interface: Cleaner, Prettier• Better Adherence to Computing Conventions

– Mac Bundle

– 64 Bit Mac and Windows

• DICOM Networking and Database• New Layouts• Improved Modules: EMSegmenter, Annotations, …


Results: For Developers

• Rework and Modularization

• Better Software Process and Testing

• Qt: Rich Widget Library, OS Abstractions

• Cleaner Abstractions– New Layouts– Displayable Managers

• SuperBuild

• Ports to Newer Software– Lion, Ubuntu 11.x…– VTK 5.8, (ITKv4)…• CTK: Uses OPM (Other People’s Money)– International Developer Community– We Contribute Non-Slicer-Specific Developments


Slicer 4.0 Highlights

QIN Multiparametric Prostate Imaging (Fedorov, Fennessy) Using CompareView



• EMSegmenter– Command

Line– Easy Wizard– Fully

Customizable Interface



• DICOM Networking and Database– DICOM Listener, Query/Retrieve, Send– Local Cache, Thumbnails, Series Selection…



• Volume Rendering– 2D-3D ROI

– GPU Ray Casting

• MRML Configuration for use in Modules



New Annotation Infrastructure with Hierarchies



• Atlas and Model Hierarchy Support



• Diffusion Support– Improved

Performance– DICOM to Full

Brain Tractography Wizard


Results: Slicer4 Download Stats

• New Download Infrastructure– Easier for Users– Better Analytics– Thanks to Zach Mullen and Mike Halle

• Data Collected So Far– 11/28/11 (RSNA) to 1/11/12 (Yesterday)– Robots Removed from Statistics

– 4713 Total Downloads in 45 Days

– Rate of over 38,000 / Year, 100 / Day


Slicer 4.0 Impact: First 45 Days


What’s Next?

• 3D Slicer 4.0.1: Today• 3D Slicer 4.1

– Summer 2012 Project Week– ITK v 4

• 3D Slicer 4.2– RSNA 2012

• Patch Releases Approximately Yearly– Active/Unstable Developments as Extensions


Priorities

• Maintenance: ITKv4, Stability, Documentation, Performance…

• Extensibility: Extension Modules, Scripting

• DICOM: Radiation Therapy, Structured Reporting, Diffusion, Network

• Interactive Editing• Annotations, Model and Display

Hierarchies


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2

5

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Core 1b – Engineering5 Aims / 5 Platforms

Architecture – tools, operating paradigms, reporting mechanisms, integration points

End-user platform – interactive methods and information visualization for longitudinal analysis, exploratory data analysis, and translational research

Computational platform – stream processing, cloud computing, statistical analysis, informatics, machine learning

Data management – non-imaging and derived data, DICOM and cloud services

Software engineering and software quality – navigable timeline for revision control, build, test, documentation and release

core 1b – engineering end-user platform

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