Epson V700 Scanner: Add plate detection and colony phenotyping pipeline - #75

Merged

lanery merged 28 commits into

rl/v700-plate-detection

May 18, 2026

Commits on May 8, 2026

Epson V700 Scanner: Replace deprecated skimage.io with imageio.v3

lanery
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cursoragent
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82cac5e

Commits on May 9, 2026

Epson V700 Scanner: Add plate detection and rename TIFFToJPEGConverter to TiffProcessor

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2d16f8c
Epson V700 Scanner: Review fixes for plate detection pipeline

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0015ec5

Commits on May 11, 2026

Make detect_plates an instance method
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88e4a74
Epson V700 Scanner: Clean up TiffProcessor API and edge cases

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cursoragent
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9221dd3
Epson V700 Scanner: Add colony detection and phenotyping pipeline

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b320b28
Epson V700 Scanner: Add colony overlay visualization and CSV export

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8245899
Epson V700 Scanner: Draw colony contours on the main export JPEG

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ce086b7
Epson V700 Scanner: Use fixed pixel margin for colony detection crop

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8fe5c8e
Epson V700 Scanner: Source colony margin from single constant

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198a3c5
Epson V700 Scanner: Use 99.5th percentile for colony presence check

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ec96c3f
Epson V700 Scanner: Replace Gaussian smoothing with Difference-of-Gaussians

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265793b
Update colony_detection.py
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f60d136
Fix colony detection tests broken by MARGIN_PX increase to 200

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9b07bab
Update colony_detection.py
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4e9b9b5

Commits on May 15, 2026

Update image_processing.py
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e2222a2

Commits on May 18, 2026

Colony detection: switch to physical units (mm) and collect RGB

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c9d5bf7
Colony detection: exclude border-touching colonies via clear_border

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9464bf3
Revert "Colony detection: exclude border-touching colonies via clear_border"
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1aa24f3
Colony detection: remove border-touching colonies with clear_border

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57764a6
Return cleaned mask from measure_colonies for contour overlay

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501fffb
Refactor colony overlay from contour drawing to labeled bounding boxes

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6d2f51a
Colony detection: discard colonies smaller than 0.05 mm²

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dad1f82
Hide colony labels when plate has >300 colonies to reduce clutter

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26b3a53
Update colony_detection.py
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84e27f1
Unify colony detection pipeline into single shared entry point

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c2e93bf
Merge branch 'staging' into rl/v700-plate-detection
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0e3b19e
Fix RGBA conversion, cache RGB, harden parse_metadata, and add tests

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13d35e8