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angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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ezSegmentation #958

Closed srivarra closed 11 months ago

srivarra commented 1 year ago

If you haven't already, please read through our contributing guidelines before opening your PR

What is the purpose of this PR?

Adds ezSegmentation functionality. This PR will add many of the backend features. The notebook and interactive Jupyter components will come in a separate PR.

How did you implement your changes

Currently added the following files:

Remaining issues

Need to add the rest of the stuff in #847, #907.

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alex-l-kong commented 1 year ago

Mostly general formatting stuff in the new ezSegmenter notebook. Main points to keep in mind are to:

  1. Combine certain cells into one
  2. Documentation should be done in markdown cells, not code comments
  3. Remove cell outputs, other than example images.
alex-l-kong commented 11 months ago

@srivarra looks like the tests for ez_object_segmentation.py are still failing. Can you look into this?