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Add x,y coords and cell size in pixels to Nimbus final results - #58

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JLrumberger merged 2 commits into
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copilot/57-nimbus-downstream-analysis
Apr 21, 2026
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Add x,y coords and cell size in pixels to Nimbus final results#58
JLrumberger merged 2 commits into
mainfrom
copilot/57-nimbus-downstream-analysis

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Copilot AI commented Apr 17, 2026

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Summary

Closes issue #57 by adding cell centroid coordinates (x, y) and cell size (area in pixels) to the Nimbus cell table output, making these spatial properties available for downstream analysis.

Changes

  • src/nimbus_inference/utils.py:

    • Added 'area' to the regionprops_table properties in segment_mean() (centroid was already included)
    • In predict_fovs(), extracted centroid_x, centroid_y, and area columns from the regionprops output and added them to the per-FOV DataFrame
  • tests/test_utils.py:

    • Updated expected column sets in test_predict_fovs to include centroid_x, centroid_y, and area

Output columns

The cell table now includes these additional columns:

Column Description
centroid_x X coordinate (column) of cell centroid in pixels
centroid_y Y coordinate (row) of cell centroid in pixels
area Cell size in pixels

Copilot AI and others added 2 commits April 17, 2026 15:14
@JLrumberger
JLrumberger marked this pull request as ready for review April 21, 2026 08:13
@JLrumberger
JLrumberger merged commit 69866bc into main Apr 21, 2026
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@JLrumberger
JLrumberger deleted the copilot/57-nimbus-downstream-analysis branch April 21, 2026 08:13
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2 participants