Difference between revisions of "Explore integration of Web-based imaging workflows with Slicer"

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Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
 
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Image:Slicer connected workflow.png | Workflow to read from SlicerWeb with downstream processing
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Image:Outimage.png|Image as received from SlicerWeb
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Image:Rotated and blurred.png | Result after running workflow
 
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<!-- Objective bullet points -->
 
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* Explore how Slicer can interact with an existing web-based, open-source workflow system (Flow, developed by Kitware and KnowledgeVis, LLC)
 
* Explore how Slicer can interact with an existing web-based, open-source workflow system (Flow, developed by Kitware and KnowledgeVis, LLC)
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* Exchange data between 3D Slicer and the Flow workflow system
 
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<!-- Approach and Plan bullet points -->
 
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* Evaluate SimpleITK vs. scikit-image as imaging toolkit for the workflow system. 
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* Load a MRML scene into Slicer and read images into Flow by accessing through Slicer's RestAPI
* Connect with Girder-breakout team to discuss data sharing between systems
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* Use Steve's (work in progress) SlicerWeb Extension to respond to REST requests from Flow
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* Connect with Girder-breakout team to discuss data sharing between systems (Slicer, Girder, Flow, etc.)
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* (after project week), expand to work for whole NRRD image that comes from the REST API.
 
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<!-- Progress and Next steps bullet points (fill out at the end of project week) -->
 
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* Hosted Slicer locally and was able to reach the REST API, extracting
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* Retrieved a 2D Slice from Slicer and automatically ran it through a small workflow
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* Next step would be to retrieve named volumes as 3D NRRD format from the SlicerWeb
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* Productive discussions were conducted with the NiPype team regarding how to utilize the Flow engine as an interface for NiPype-executed computation
 
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Latest revision as of 13:23, 13 January 2017

Home < Explore integration of Web-based imaging workflows with Slicer

Key Investigators

  • Curt Lisle, KnowledgeVis, LLC

Project Description

Objective Approach and Plan Progress and Next Steps
  • Explore how Slicer can interact with an existing web-based, open-source workflow system (Flow, developed by Kitware and KnowledgeVis, LLC)
  • Exchange data between 3D Slicer and the Flow workflow system
  • Load a MRML scene into Slicer and read images into Flow by accessing through Slicer's RestAPI
  • Use Steve's (work in progress) SlicerWeb Extension to respond to REST requests from Flow
  • Connect with Girder-breakout team to discuss data sharing between systems (Slicer, Girder, Flow, etc.)
  • (after project week), expand to work for whole NRRD image that comes from the REST API.
  • Hosted Slicer locally and was able to reach the REST API, extracting
  • Retrieved a 2D Slice from Slicer and automatically ran it through a small workflow
  • Next step would be to retrieve named volumes as 3D NRRD format from the SlicerWeb
  • Productive discussions were conducted with the NiPype team regarding how to utilize the Flow engine as an interface for NiPype-executed computation

Background and References

The Flow source code is available here: https://github.com/Kitware/flow