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melonora / napari-cell-gater

A napari plugin for cell marker gating.
BSD 3-Clause "New" or "Revised" License
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create snapshots of positive cells #23

Open josenimo opened 2 months ago

josenimo commented 2 months ago

The idea is to show a sneak peak of the gating via a .png, people would show this in ppts.

Assumptions for automation:

  1. User provides csvs, images, and gates
  2. For each marker:
  3. Look for a bounding box of 1000x1000px, in which both a positive and negative cell are present.
  4. Create plot where, nuclear stain, mask outlines, and marker are overlayed, positive cells have points on them. ISSUE: Which contrast settings to use? Could we save the range of the histogram for each marker for each sample into the gates csv, and use this info?
  5. Create .png snapshots for each marker/sample combination.
josenimo commented 2 months ago

Metadata is important. Which histogram settings are being shown? Which pixels are being shown? Which marker? Which resolution/magnification? How common are these cells? How deterministic is this? If someone does the same would it show the same snapshot?