Automatic prompt generator #1122
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anwai98
reviewed
Nov 24, 2025
anwai98
reviewed
Nov 24, 2025
constantinpape
commented
Nov 24, 2025
…tational-cell-analytics/micro-sam into automatic-prompt-generator
…tational-cell-analytics/micro-sam into automatic-prompt-generator
…tational-cell-analytics/micro-sam into automatic-prompt-generator
* Use stability score in nms * Update baseline submission scripts and add more datasets * Implement box prompt derivation * Add more datasets * Make pipeline modular and add more datasets * Change prompt type defaults * Update analysis scripts * More updates to posthoc analysis * Better center derivation for point prompts from connected components * Finish up processing data * Add center cropping strategy * Finalize data processing and submission * Minor fixes to SAM2 and SAM3 pipelines * Remove other baselines and add preliminary plotting scripts * Push current code state * Update logit thresholding logic * Update visualization scripts * Implement intersection over min * Push more changes * Push current updates for new grid search * Add box prompt refinement * Add plotting scripts --------- Co-authored-by: anwai98 <[email protected]>
* Refactor APG interface and instance segmentation tests * Working version of tiled auto prompt generation * Refactor instance segmentation output logic * Rename 'get_amg' * Fix automatic segmentation tests * Fix tests * Parallelize operations in apg processing * Minor updates * Make inference for WSIs more efficient WIP * Implement memory efficient mode for APG inference * Debug stitching * Add changes to experiment running for box prompt refinement * Minor script update --------- Co-authored-by: anwai98 <[email protected]>
Implement tiled embedding prediction and segmentation
…tational-cell-analytics/micro-sam into automatic-prompt-generator
Update image preprocessing in _to_image
…tational-cell-analytics/micro-sam into automatic-prompt-generator
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I have updated the documentation and some logic in |
anwai98
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Dec 19, 2025
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anwai98
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There's some local docstrings missing for functionalities related to APG, but we can take care of it in another round once this is merged to dev!
The changes look good to me here. Let's merge it once the tests look good!
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