Fix organoid segmentation #44

MikeLippincott · 2025-05-09T03:39:23Z

This PR adds critical functionality that scans an image for the largest object possible to segment across a dynamic range for whole organoid segmentation.

* inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments

review-notebook-app · 2025-05-09T03:39:27Z

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Pull Request Overview

This PR fixes organoid segmentation by adding a recursive segmentation function and updating hardcoded parameters for whole organoid segmentation. Key changes include:

Renaming of hardcoded parameters such as well_fov and compartment in multiple scripts.
Introduction of the recursive function segment_with_diameter with dynamic diameter reduction.
Updates to notebook cell execution metadata and output messages.

Reviewed Changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 1 comment.

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File	Description
2.segment_images/scripts/7.clean_up_segmentation.py	Updated cell indices in notebook run code.
2.segment_images/scripts/4.reconstruct_3D_masks.py	Changed well_fov and compartment values to support organoid segmentation.
2.segment_images/scripts/3.segmentation_decoupling.py	Modified well_fov and compartment values for organoid segmentation.
2.segment_images/scripts/2.segment_whole_organoids.py	Added segment_with_diameter and updated segmentation flow and parameters.
2.segment_images/scripts/0.segment_nuclei_organoids.py	Adjusted well_fov for proper path setup in notebook mode.
2.segment_images/notebooks/7.clean_up_segmentation.ipynb	Updated execution counts and output messages for consistency.

Comments suppressed due to low confidence (1)

2.segment_images/scripts/2.segment_whole_organoids.py:308

[nitpick] The variable 'slice' shadows a built-in Python name. Consider renaming it (e.g., 'img_slice') to improve code clarity and prevent potential confusion.

for slice in tqdm.tqdm(range(imgs.shape[0])):

Copilot · 2025-05-09T03:39:51Z

2.segment_images/scripts/2.segment_whole_organoids.py

+
+    if labels is None:
+        print(f"Labels are empty for diameter {diameter}. Trying smaller diameter...")
+        return segment_with_diameter(img, model, channels, z_axis, diameter - 250)


The recursive call passes parameters in an incorrect order; the function expects diameter as the third argument, so it should be called as segment_with_diameter(img, model, diameter - 250, z_axis, channels).

Suggested change

return segment_with_diameter(img, model, channels, z_axis, diameter - 250)

return segment_with_diameter(img, model, diameter - 250, z_axis, channels)

2.segment_images/scripts/2.segment_whole_organoids.py

* Initial commit * inital commit + preprocessing (WayScience#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments

* Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress capture * add the documentation * feature walkthrough * feature walkthrough * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]>

* Initial commit * inital commit + preprocessing (WayScience#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments

* Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress capture * add the documentation * feature walkthrough * feature walkthrough * progress capture * progress capture * progress capture * progress capture * chaos commit - will clean up soon c: * need to clean up + rerun * segmentations revamped * post-hoc reassignments * align labels * nbconvert * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * progress capture * add the documentation * feature walkthrough * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]>

* Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress capture * add the documentation * feature walkthrough * feature walkthrough * progress capture * progress capture * progress capture * progress capture * chaos commit - will clean up soon c: * need to clean up + rerun * segmentations revamped * post-hoc reassignments * align labels * nbconvert * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * progress capture * add the documentation * feature walkthrough * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * fix neighbors and granularity * addressing comments --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]>

* Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress capture * add the documentation * feature walkthrough * feature walkthrough * progress capture * progress capture * progress capture * progress capture * chaos commit - will clean up soon c: * need to clean up + rerun * segmentations revamped * post-hoc reassignments * align labels * nbconvert * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * progress capture * add the documentation * feature walkthrough * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * redo shell script * redo shell script * test nf on HPC * adjusting pipe * adjusting pipe * adjusting pipe * adjusting pipe * adjusting pipe * adjusting pipe * adjusting pipe * update the nf * update the nf * update nf * update nf config * update nf config * update nf config * update nf config * update nf config * update nf config * fixing nf pipeline * addressing comments --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]>

* Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress capture * add the documentation * feature walkthrough * feature walkthrough * progress capture * progress capture * progress capture * progress capture * chaos commit - will clean up soon c: * need to clean up + rerun * segmentations revamped * post-hoc reassignments * align labels * nbconvert * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * progress capture * add the documentation * feature walkthrough * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * progress capture * run the sc profile merge * run IBP merges * update profiles * addressing comments --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]>

* Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress capture * add the documentation * feature walkthrough * feature walkthrough * progress capture * progress capture * progress capture * progress capture * chaos commit - will clean up soon c: * need to clean up + rerun * segmentations revamped * post-hoc reassignments * align labels * nbconvert * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * progress capture * add the documentation * feature walkthrough * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * feature extraction fixes * redo profiling * redo the coloc * rerun coloc * rerun coloc * run areashape again * git add new profilers * run segs on HPC * fix the clean up * fixing slews of bugs * remove old scripts * switch to duckdb * fix the areashape featurization * fix pathing * runcellprofiler cleanup * checking files * addressing comments * feature extraction fixes * redo profiling * redo the coloc * rerun coloc * rerun coloc * run areashape again * git add new profilers * run segs on HPC * fix the clean up * fixing slews of bugs * remove old scripts * switch to duckdb * fix the areashape featurization * fix pathing * runcellprofiler cleanup * checking files * addressing comments --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]>

* Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress capture * add the documentation * feature walkthrough * feature walkthrough * progress capture * progress capture * progress capture * progress capture * chaos commit - will clean up soon c: * need to clean up + rerun * segmentations revamped * post-hoc reassignments * align labels * nbconvert * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * progress capture * add the documentation * feature walkthrough * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * feature extraction fixes * redo profiling * redo the coloc * rerun coloc * rerun coloc * run areashape again * git add new profilers * run segs on HPC * fix the clean up * fixing slews of bugs * remove old scripts * switch to duckdb * fix the areashape featurization * fix pathing * runcellprofiler cleanup * checking files * addressing comments * progress capture * relating sc and organoids * add script * addressing comments --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]>

* Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress capture * add the documentation * feature walkthrough * feature walkthrough * progress capture * progress capture * progress capture * progress capture * chaos commit - will clean up soon c: * need to clean up + rerun * segmentations revamped * post-hoc reassignments * align labels * nbconvert * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * progress capture * add the documentation * feature walkthrough * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * feature extraction fixes * redo profiling * redo the coloc * rerun coloc * rerun coloc * run areashape again * git add new profilers * run segs on HPC * fix the clean up * fixing slews of bugs * remove old scripts * switch to duckdb * fix the areashape featurization * fix pathing * runcellprofiler cleanup * checking files * addressing comments * featurization decoupled * Update 3.cellprofiling/featurization_utils/errors.py Co-authored-by: Copilot <[email protected]> * Update 3.cellprofiling/scripts/area_shape.py Co-authored-by: Copilot <[email protected]> * addressing comments --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]>

* Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress capture * add the documentation * feature walkthrough * feature walkthrough * progress capture * progress capture * progress capture * progress capture * chaos commit - will clean up soon c: * need to clean up + rerun * segmentations revamped * post-hoc reassignments * align labels * nbconvert * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * progress capture * add the documentation * feature walkthrough * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * feature extraction fixes * redo profiling * redo the coloc * rerun coloc * rerun coloc * run areashape again * git add new profilers * run segs on HPC * fix the clean up * fixing slews of bugs * remove old scripts * switch to duckdb * fix the areashape featurization * fix pathing * runcellprofiler cleanup * checking files * addressing comments * update the organoid segmentations * addressing comments --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]>

* Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress capture * add the documentation * feature walkthrough * feature walkthrough * progress capture * progress capture * progress capture * progress capture * chaos commit - will clean up soon c: * need to clean up + rerun * segmentations revamped * post-hoc reassignments * align labels * nbconvert * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * progress capture * add the documentation * feature walkthrough * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * feature extraction fixes * redo profiling * redo the coloc * rerun coloc * rerun coloc * run areashape again * git add new profilers * run segs on HPC * fix the clean up * fixing slews of bugs * remove old scripts * switch to duckdb * fix the areashape featurization * fix pathing * runcellprofiler cleanup * checking files * addressing comments * progress capture * add umaps * add the eda * adding scripts * addressing comments --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]>

* Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress capture * add the documentation * feature walkthrough * feature walkthrough * progress capture * progress capture * progress capture * progress capture * chaos commit - will clean up soon c: * need to clean up + rerun * segmentations revamped * post-hoc reassignments * align labels * nbconvert * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * progress capture * add the documentation * feature walkthrough * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * feature extraction fixes * redo profiling * redo the coloc * rerun coloc * rerun coloc * run areashape again * git add new profilers * run segs on HPC * fix the clean up * fixing slews of bugs * remove old scripts * switch to duckdb * fix the areashape featurization * fix pathing * runcellprofiler cleanup * checking files * addressing comments * ingest more data * ingest more data * add the new patients * fixing the pathing error * fixing the pathing error * fixing the pathing error * update ingestions * addressing comments --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]>

* Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress capture * add the documentation * feature walkthrough * feature walkthrough * progress capture * progress capture * progress capture * progress capture * chaos commit - will clean up soon c: * need to clean up + rerun * segmentations revamped * post-hoc reassignments * align labels * nbconvert * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * Update 2.segment_images/scripts/5.segment_cells_watershed_method.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * progress capture * add the documentation * feature walkthrough * Ingest data (#41) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * progress catpure * progress capture * ingest data * ingest data * data ingestion and preprocessing * data ingestion * addressing comments * Run seg featurization (#39) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * run without the reslicing * run segmentation: * ready to run all segmentations for all organoids for one patient * ready to run all segmentations for all organoids for one patient * fix the profiling * fix the texturization feature extraction * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * run all organoids segmentation on HPC * rerun on HPC now that the patient IDs have been added * rerun on HPC * data ingestion and preprocessing * rerun the segs * rerun the segs * fixed bash error * add patient information to scripts * merge features * add cleanup * test with nexflow * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * testing nf * adding nextflow * adding nextflow * fix the featurization * change the profiling * run on HPC * rerun the NF0014 featurization * granularity * rerun features to get the proper profiling * update the resource profiling * prep for featurization * add the ability to run nf on HPC * add the ability to run nf on HPC * run * rm slurm files * rm slurm files * fix nf * fix nf * run each * attempt 2 * attempt 2 * testing on HPC * add each nextflow change * push to HPC: * attempt run on HPC: * run all * merge the profiles * Update 2.segment_images/child_segmentation.sh Co-authored-by: Copilot <[email protected]> * Update 1.image_quality_control/scripts/0.cp_image_qc.py Co-authored-by: Dave Bunten <[email protected]> * addressing comments * rebase --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]> * Fix organoid segmentation (#44) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * add segmentation updates * rerun segmentations * update segmentations * addressing comments * Data Ingestions (#46) * Initial commit * inital commit + preprocessing (#1) * inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments * gitignore * preprocessing * rerun on HPC * push to HPC * run all * run all * process new patient * process new patient * feature extraction fixes * redo profiling * redo the coloc * rerun coloc * rerun coloc * run areashape again * git add new profilers * run segs on HPC * fix the clean up * fixing slews of bugs * remove old scripts * switch to duckdb * fix the areashape featurization * fix pathing * runcellprofiler cleanup * checking files * addressing comments * fix pathing for repo * fix pathing * fix pathing * run all * fix featurization pathing * fix featurization pathing * run segs --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Dave Bunten <[email protected]>

MikeLippincott and others added 24 commits December 2, 2024 15:33

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inital commit + preprocessing (WayScience#1)

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Merge remote-tracking branch 'upstream/main'

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Merge remote-tracking branch 'upstream/main'

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Merge remote-tracking branch 'upstream/main'

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Merge remote-tracking branch 'upstream/main'

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Merge remote-tracking branch 'upstream/main'

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add segmentation updates

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MikeLippincott requested a review from Copilot May 9, 2025 03:39

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MikeLippincott added 2 commits May 9, 2025 07:59

rerun segmentations

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update segmentations

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d33bs approved these changes May 19, 2025

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addressing comments

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MikeLippincott merged commit c009b33 into WayScience:main May 29, 2025

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Fix organoid segmentation #44

Fix organoid segmentation #44

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MikeLippincott commented May 9, 2025

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	return segment_with_diameter(img, model, channels, z_axis, diameter - 250)
	return segment_with_diameter(img, model, diameter - 250, z_axis, channels)

Fix organoid segmentation #44

Fix organoid segmentation #44

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MikeLippincott commented May 9, 2025

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