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Cell Segmentation Tutorials #1750

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neuromusic opened this issue Jan 22, 2020 · 1 comment
Closed
10 tasks

Cell Segmentation Tutorials #1750

neuromusic opened this issue Jan 22, 2020 · 1 comment
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@mattcai

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@neuromusic
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neuromusic commented Jan 22, 2020 •
edited by mattcai
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As a single cell biologist learning about image-based transcriptomics,
I want to know how to segment cells
so that I can learn how to use starfish to process image-based transcriptomics data.

Acceptance Criteria

  1. There are tutorials that demonstrate watershed segmentation, ilastik segmentation, and importing ROIs
  2. There are howtos for all of the API components that support cell segmentation
  3. All tutorials and howtos are rendered as sphinx-gallery examples.

Tutorials

  • Segmenting cells by thresholding and watershed
  • Segmenting cells by ilastik pretrained classifier
  • Segmenting cells with imported ROIs

Howtos

  • How to use ThresholdBinarize
  • How to use MinDistanceLabel
  • How to use AreaFilter
  • How to use Merge.SimpleMerge
  • How to use morphology.Filter.Reduce
  • How to use image.Filter.Reduce
  • How to use Segment.WatershedSegment
@mattcai mattcai self-assigned this Feb 11, 2020
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closed by #1821

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