Feaurization walkthrough #40
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* inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments
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Pull Request Overview
This PR provides a walkthrough of the featurization process for organoids by updating notebook configurations and refining the file structure and pre-commit configuration.
- Updates kernel specifications and Python versions in Jupyter notebooks.
- Refactors argument parsing and formatting in the file structure update notebook.
- Updates pre-commit hook revisions for consistency and compatibility.
Reviewed Changes
Copilot reviewed 6 out of 6 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| 0.preprocessing_data/notebooks/1.make_z-stack_images.ipynb | Updated kernel display name and adjusted the Python version. |
| 0.preprocessing_data/notebooks/0.update_file_structure.ipynb | Reformatted argument parsing and function definitions; adjusted notebook metadata version. |
| .pre-commit-config.yaml | Upgraded revision numbers for pre-commit hooks to the latest tags. |
Comments suppressed due to low confidence (2)
.pre-commit-config.yaml:3
- Verify that updating the revision to v0.7.0 does not introduce any breaking changes in the pre-commit hook behavior, and document if necessary.
rev: v0.7.0
.pre-commit-config.yaml:18
- Confirm and document that the ruff version update to v0.11.8 is compatible with the current codebase and pre-commit configuration.
rev: v0.11.8
axiomcura
approved these changes
May 29, 2025
* Initial commit * inital commit + preprocessing (WayScience#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
* Initial commit * inital commit + preprocessing (WayScience#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]>
* 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 (WayScience#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
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This PR is a walk through of the featurization of the organoids.
The notebook describes the feature space and how many features are extracted for each organoid.
I recommend using ReviewNB for this PR.