Difference between revisions of "Project Week 25/DICOM Segmentation Support for Cornerstone and OHIF Viewer"

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Back to [[Project_Week_25#Projects|Projects List]]
 
Back to [[Project_Week_25#Projects|Projects List]]
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==Key Investigators==
 
==Key Investigators==
 
<!-- Key Investigator bullet points -->
 
<!-- Key Investigator bullet points -->
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*Erik Ziegler (Open Health Imaging Foundation)
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*Erik Ziegler (Open Health Imaging Foundation, USA)
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*Steve Pieper  (Isomics, Inc.)
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*[http://www.spl.harvard.edu/pages/People/pieper Steve Pieper] (Isomics, Inc., USA)
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*Marco Nolden  (DKFZ)
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*[https://www.dkfz.de/en/mic/team/people/Marco_Nolden.html Marco Nolden] (German Cancer Research Center (DKFZ), Germany)
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*[http://www.spl.harvard.edu/pages/People/tkapur Tina Kapur]  (Brigham and Women's Hospital, Harvard Medical School)
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*[http://www.spl.harvard.edu/pages/People/tkapur Tina Kapur]  (Brigham and Women's Hospital, Harvard Medical School, USA)
  
 
==Project Description==
 
==Project Description==
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** Needs suite of editing tools (plugin architecture)
 
** Needs suite of editing tools (plugin architecture)
 
** Needs DICOM Segmentation object support
 
** Needs DICOM Segmentation object support
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** Needs DICOM Structured Report container for image measurements (lines, points, ROIs)
 
|<!-- Approach and Plan bullet points -->
 
|<!-- Approach and Plan bullet points -->
 
* Review architectures and experiments so far
 
* Review architectures and experiments so far
 
** SAKE viewer tool (http://sakeviewer.com/)
 
** SAKE viewer tool (http://sakeviewer.com/)
 
** Experiments with Segmentation read/write in javascript
 
** Experiments with Segmentation read/write in javascript
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** Discussions and prototypes with Dana Farber
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** Discussions and prototypes with Dana-Farber Cancer Institute
 
* Try building an end-to-end proof of concept
 
* Try building an end-to-end proof of concept
 
** Read grayscale and segmentation
 
** Read grayscale and segmentation
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* What other work is needed
 
* What other work is needed
 
|<!-- Progress and Next steps (fill out at the end of project week), bullet points -->
 
|<!-- Progress and Next steps (fill out at the end of project week), bullet points -->
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*Progress
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** Added layered image support to Cornerstone master (version 0.12.1)
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*** User-controls colormap, opacity, and visibility
 +
** Added layered image stack support to Cornerstone Tools (version 0.9.0)
 +
** Created '''dcmjs''' repository (https://github.com/pieper/dcmjs) to release Steve's client-side DICOM I/O support
 +
** Created examples for DICOM Segmentation (binary only) display and creation from the browser
 +
** Discussed plans for client-side Structured Report export
 +
* Next Steps
 +
* Bug fixing for layer support in Cornerstone and Cornerstone Tools
 +
* Fix brush tool to store drawings on multiple images
 +
* Cleanup dcmjs examples to allow user-uploaded data
 +
* Cleanup dcmjs repository to release as a usable library
 +
* Use dcmjs for client-side sorting of uploaded files, link this to OHIF Standalone Viewer
 
|}
 
|}
  
 
==Illustrations==
 
==Illustrations==
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[[File:OHIF Study List.png]]
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[[image:OHIF Study List.png|800px]]
  
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[[File:OHIF Viewer Screenshot.png]]
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[[image:OHIF Viewer Screenshot.png|800px]]
  
 
==Background and References==
 
==Background and References==
  
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SIIM2017 Learning Lab introduction to Cornerstone / OHIF:
+
SIIM2017 Learning Lab introduction to Cornerstone / OHIF
 
* Slides: https://www.dropbox.com/s/bg4mm7s9kek0708/SIIM2017%20-%20Build%20your%20own%20zero%20footprint%20web%20viewer.pptx?dl=1
 
* Slides: https://www.dropbox.com/s/bg4mm7s9kek0708/SIIM2017%20-%20Build%20your%20own%20zero%20footprint%20web%20viewer.pptx?dl=1
 
* Repository: https://github.com/chafey/byozfwv
 
* Repository: https://github.com/chafey/byozfwv
  
−
OHIF Community Forum Slides:
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OHIF Community Forum Slides
 
* https://docs.google.com/presentation/d/1iYZoU7v7KHSLHiKwH1_9_wweAkG7RGnyxrWeeHva4zQ/edit#slide=id.g17e0507313_1_46
 
* https://docs.google.com/presentation/d/1iYZoU7v7KHSLHiKwH1_9_wweAkG7RGnyxrWeeHva4zQ/edit#slide=id.g17e0507313_1_46
 
* https://docs.google.com/presentation/d/1K9Y6eP5DYTXoDlfwCZE6GkCUp83AK4_40YQS0dlzVBo/edit#slide=id.g17df770847_0_0
 
* https://docs.google.com/presentation/d/1K9Y6eP5DYTXoDlfwCZE6GkCUp83AK4_40YQS0dlzVBo/edit#slide=id.g17df770847_0_0
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* https://github.com/OHIF/Viewers
 
* https://github.com/OHIF/Viewers
  
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Work thus far on segmentations / overlays in Cornerstone:
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Work thus far on segmentations / overlays in Cornerstone
−
 
 
 
* https://github.com/chafey/cornerstone/pull/68
 
* https://github.com/chafey/cornerstone/pull/68
 
* https://github.com/chafey/cornerstone/pull/109
 
* https://github.com/chafey/cornerstone/pull/109
 
* https://rawgit.com/swederik/cornerstone/composition/example/testSeg/index.html
 
* https://rawgit.com/swederik/cornerstone/composition/example/testSeg/index.html
 
* http://sakeviewer.com/
 
* http://sakeviewer.com/
 +
 +
Progress
 +
[[File:Screen Shot 2017-06-30 at 12.55.25.png|thumb|Exporting from Cornerstone and importing into Slicer]]
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[[File:ScreenshotImportMITK.PNG|thumb|Importing into MITK]]

Latest revision as of 12:29, 30 June 2017

Home < Project Week 25 < DICOM Segmentation Support for Cornerstone and OHIF Viewer


Back to Projects List

Key Investigators

  • Erik Ziegler (Open Health Imaging Foundation, USA)
  • Steve Pieper (Isomics, Inc., USA)
  • Marco Nolden (German Cancer Research Center (DKFZ), Germany)
  • Tina Kapur (Brigham and Women's Hospital, Harvard Medical School, USA)

Project Description

Objective Approach and Plan Progress and Next Steps
  • Overall goal is to facilitate zero-footprint image annotation
    • Runs in browser
    • Fast and usable by clinicians
    • Interoperable (DICOM-based)
  • Cornerstone has great platform
    • Needs segmentation display
    • Needs suite of editing tools (plugin architecture)
    • Needs DICOM Segmentation object support
    • Needs DICOM Structured Report container for image measurements (lines, points, ROIs)
  • Review architectures and experiments so far
    • SAKE viewer tool (http://sakeviewer.com/)
    • Experiments with Segmentation read/write in javascript
    • Discussions and prototypes with Dana-Farber Cancer Institute
  • Try building an end-to-end proof of concept
    • Read grayscale and segmentation
    • Edit segmentation
    • Write out segmentation (store to server)
  • Discuss how to harden and integrate with production systems
  • What other work is needed
  • Progress
    • Added layered image support to Cornerstone master (version 0.12.1)
      • User-controls colormap, opacity, and visibility
    • Added layered image stack support to Cornerstone Tools (version 0.9.0)
    • Created dcmjs repository (https://github.com/pieper/dcmjs) to release Steve's client-side DICOM I/O support
    • Created examples for DICOM Segmentation (binary only) display and creation from the browser
    • Discussed plans for client-side Structured Report export
  • Next Steps
  • Bug fixing for layer support in Cornerstone and Cornerstone Tools
  • Fix brush tool to store drawings on multiple images
  • Cleanup dcmjs examples to allow user-uploaded data
  • Cleanup dcmjs repository to release as a usable library
  • Use dcmjs for client-side sorting of uploaded files, link this to OHIF Standalone Viewer

Illustrations

OHIF Study List.png

OHIF Viewer Screenshot.png

Background and References

SIIM2017 Learning Lab introduction to Cornerstone / OHIF

OHIF Community Forum Slides

Repositories

Work thus far on segmentations / overlays in Cornerstone

Progress

Exporting from Cornerstone and importing into Slicer
Importing into MITK
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