Difference between revisions of "2016 Winter Project Week/Projects/DigitalPathologyNuclearSegmentation"

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==Key Investigators==
 
==Key Investigators==
 
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* Erich Bremer - [https://bmi.stonybrookmedicine.edu/ Stony Brook University]
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* Yi Gao - [https://bmi.stonybrookmedicine.edu/ Stony Brook University]
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* Nicole Aucoin - [http://www.brighamandwomens.org/ Brigham and Women's Hospital]
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* Andrey Fedorov - [http://www.brighamandwomens.org/ Brigham and Women's Hospital]
  
 
==Project Description==
 
==Project Description==
 
{| class="wikitable"
 
{| class="wikitable"
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! style="text-align: left; width:27%" |  Objective
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! style="text-align: left; width:27%" |  Approach and Plan
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! style="text-align: left; width:27%" |  Progress and Next Steps
 
|- style="vertical-align:top;"
 
|- style="vertical-align:top;"
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! style="text-align: left; width:27%" |       Objective
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|
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<!-- Add a bulleted list of key points -->
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<!-- Objective bullet points -->
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*  
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* Create intuitive and user-friendly GUI
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* make meta-data exportable
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! style="text-align: left; width:27%" |       Approach, Plan
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* Prepare extension for Phase II cloud work and future modules
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<!-- Add a bulleted list of key points -->
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|
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*  
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<!-- Approach and Plan bullet points -->
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* create work-flow module walking user through needed steps
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! style="text-align: left; width:27%" |     Progress
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* wrap editor module to allow for customization for segmentation purposes without interfering with global editor instance
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<!-- Fill this out at the end of Project Week; describe what you did this week and what you plan to do next -->
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* capture needed data elements and export them as [http://www.w3.org/TR/json-ld/ JSON-LD] supplementing exporting of masks
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*
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* augment GUI by requesting authentication information for [http://oauth.net/2/ OAuth 2.0] and adding elements for image selection via web.
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* refactor existing extension modules into separate distinct editor effects modules (currently lumped as one)
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|
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<!-- Progress and Next steps bullet points (fill out at the end of project week -->
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* initial work-flow module created
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* editor module wrapped and including in one of the step tabs of the work-flow module
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* label mask saved, still need to add additional meta data (algorithm parameters) as JSON-LD export
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* username/password entries added to work-flow module for future web authentication
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* original single editor-effect refactored into separate effects.  Further cleaning of of code needed
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* future work - allow image tiles to be select via web interface and resultant label masks and meta data to be exported directly to web services using OAuth2 authenication
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* remove unneeded GUI elements and set additional field automatically.  Create better tab icons!
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* test SlicerPathology with new OpenCV Extension
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|}
  
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|}
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[[File:SlicerPathologybeginworkweek2016.png|600px|thumb|left|SlicerPathology extension at the start of Winter Work Week 2016]]
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[[File:Afterworkweek.png|600px|thumb|left|SlicerPathology extension at the end of Winter Work Week 2016]]
  
 
==Background and References==
 
==Background and References==
 
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data -->
 
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data -->
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* [https://github.com/SBU-BMI/SlicerPathology SlicerPathology extension source repository]
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* [http://interactivemedical.org/imic2014/CameraReadyPapers/Paper%204/IMIC_ID4_FastGrowCut.pdf Fast Growcut]

Latest revision as of 13:56, 8 January 2016

Home < 2016 Winter Project Week < Projects < DigitalPathologyNuclearSegmentation

Key Investigators

Project Description

Objective Approach and Plan Progress and Next Steps
  • Create intuitive and user-friendly GUI
  • make meta-data exportable
  • Prepare extension for Phase II cloud work and future modules
  • create work-flow module walking user through needed steps
  • wrap editor module to allow for customization for segmentation purposes without interfering with global editor instance
  • capture needed data elements and export them as JSON-LD supplementing exporting of masks
  • augment GUI by requesting authentication information for OAuth 2.0 and adding elements for image selection via web.
  • refactor existing extension modules into separate distinct editor effects modules (currently lumped as one)
  • initial work-flow module created
  • editor module wrapped and including in one of the step tabs of the work-flow module
  • label mask saved, still need to add additional meta data (algorithm parameters) as JSON-LD export
  • username/password entries added to work-flow module for future web authentication
  • original single editor-effect refactored into separate effects. Further cleaning of of code needed
  • future work - allow image tiles to be select via web interface and resultant label masks and meta data to be exported directly to web services using OAuth2 authenication
  • remove unneeded GUI elements and set additional field automatically. Create better tab icons!
  • test SlicerPathology with new OpenCV Extension
SlicerPathology extension at the start of Winter Work Week 2016
SlicerPathology extension at the end of Winter Work Week 2016

Background and References

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