Running segmentation by MikeLippincott · Pull Request #139 · WayScience/NF1_3D_organoid_profiling_pipeline

MikeLippincott · 2026-03-24T18:14:26Z

This PR updates segmentation for our final run.

I have kept nuclei segmentation the same.
I decoupled the cell/cytoplasm segmentation from the organoid segmentation. I applied the nuclei 2.5D segmentation approach to the organoid segmentation approach.

I cleaned up the segmentation module.

* ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com>

* running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * set up technical analysis * update gitignore * progress capture for tech analysis * tech analysis add files * add HPC version * add HPC version * fix the script * add updates * update HPC script * compute metrics for basicpy across scopes * addressing comments + refactor * Add basicpy code to test IC on 3D data (WayScience#118) * add basicpy code to test IC on 3D data * update code per PR review * Add first draft of areashape 3D figure (WayScience#114) * add first draft of areashape 3D figure * fix pathing for image * add another option + edits * final figure updates * Update docs (WayScience#124) * add mermaid * add mermaid to sphinx env * minor updates to capitalization * clarity facelift * remove workflow diagram * add mermaid to docs requirements * stabilize url * Update docs/source/overview.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * Update docs/source/overview.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * myst mds * fix redirects * remove broken link check too flimsy!! --------- Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * Remove unwanted modules (WayScience#122) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor and remove --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * update gitignore * Refactor qc module (WayScience#120) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor qc * add scripts * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Refactor featurization (WayScience#121) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * add refactored featurization * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update docs/RFC-2119-Feature-Naming-Convention.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Tests for featurization module (WayScience#128) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update gitignore * pytests * add test updates * adding tests * addressing comments and cleaning up tests --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Nucleo centric feature extraction (WayScience#131) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update gitignore * implement the nucleo_centric_approach! * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * progress capture * progress capture * updadting segmentations * addressing comments * Docs, tests, and utils refactor (WayScience#116) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update docs and tests and src * Update src/featurization_utils/sammed3d_featurizer.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments * switch to mystic * addressing comments * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Preprocess refactor (WayScience#117) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * software gardening of preprocessing * add preprocces step * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Onboard new data (WayScience#119) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * adding refactor * updating scripts * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Remove unwanted modules (WayScience#122) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor and remove --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Refactor featurization (WayScience#121) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * add refactored featurization * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update docs/RFC-2119-Feature-Naming-Convention.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * new plots * add new figures * addressing comments: * update table2 * Update figures/table2/scripts/table2.py Co-authored-by: Cameron Mattson <92554334+MattsonCam@users.noreply.github.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com> Co-authored-by: Gregory Way <gregory.way@gmail.com> Co-authored-by: Cameron Mattson <92554334+MattsonCam@users.noreply.github.com>

* running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * set up technical analysis * update gitignore * progress capture for tech analysis * tech analysis add files * add HPC version * add HPC version * fix the script * add updates * update HPC script * compute metrics for basicpy across scopes * addressing comments + refactor * Add basicpy code to test IC on 3D data (WayScience#118) * add basicpy code to test IC on 3D data * update code per PR review * Add first draft of areashape 3D figure (WayScience#114) * add first draft of areashape 3D figure * fix pathing for image * add another option + edits * final figure updates * Update docs (WayScience#124) * add mermaid * add mermaid to sphinx env * minor updates to capitalization * clarity facelift * remove workflow diagram * add mermaid to docs requirements * stabilize url * Update docs/source/overview.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * Update docs/source/overview.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * myst mds * fix redirects * remove broken link check too flimsy!! --------- Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * Remove unwanted modules (WayScience#122) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor and remove --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * update gitignore * Refactor qc module (WayScience#120) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor qc * add scripts * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Refactor featurization (WayScience#121) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * add refactored featurization * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update docs/RFC-2119-Feature-Naming-Convention.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Tests for featurization module (WayScience#128) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update gitignore * pytests * add test updates * adding tests * addressing comments and cleaning up tests --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Nucleo centric feature extraction (WayScience#131) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update gitignore * implement the nucleo_centric_approach! * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * progress capture * progress capture * updadting segmentations * addressing comments * Docs, tests, and utils refactor (WayScience#116) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update docs and tests and src * Update src/featurization_utils/sammed3d_featurizer.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments * switch to mystic * addressing comments * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Preprocess refactor (WayScience#117) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * software gardening of preprocessing * add preprocces step * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Onboard new data (WayScience#119) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * adding refactor * updating scripts * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Remove unwanted modules (WayScience#122) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor and remove --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Refactor featurization (WayScience#121) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * add refactored featurization * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update docs/RFC-2119-Feature-Naming-Convention.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * new plots * add new figures * addressing comments: * fix featurization, fix tests, and fix profiling * changes to featurization * changes to featurization * run on HPC * add uv * adding features * adding features * new features * add features * address comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com> Co-authored-by: Gregory Way <gregory.way@gmail.com>

* running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * set up technical analysis * update gitignore * progress capture for tech analysis * tech analysis add files * add HPC version * add HPC version * fix the script * add updates * update HPC script * compute metrics for basicpy across scopes * addressing comments + refactor * Add basicpy code to test IC on 3D data (WayScience#118) * add basicpy code to test IC on 3D data * update code per PR review * Add first draft of areashape 3D figure (WayScience#114) * add first draft of areashape 3D figure * fix pathing for image * add another option + edits * final figure updates * Update docs (WayScience#124) * add mermaid * add mermaid to sphinx env * minor updates to capitalization * clarity facelift * remove workflow diagram * add mermaid to docs requirements * stabilize url * Update docs/source/overview.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * Update docs/source/overview.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * myst mds * fix redirects * remove broken link check too flimsy!! --------- Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * Remove unwanted modules (WayScience#122) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor and remove --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * update gitignore * Refactor qc module (WayScience#120) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor qc * add scripts * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Refactor featurization (WayScience#121) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * add refactored featurization * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update docs/RFC-2119-Feature-Naming-Convention.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Tests for featurization module (WayScience#128) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update gitignore * pytests * add test updates * adding tests * addressing comments and cleaning up tests --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Nucleo centric feature extraction (WayScience#131) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update gitignore * implement the nucleo_centric_approach! * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * progress capture * progress capture * updadting segmentations * addressing comments * Docs, tests, and utils refactor (WayScience#116) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update docs and tests and src * Update src/featurization_utils/sammed3d_featurizer.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments * switch to mystic * addressing comments * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Preprocess refactor (WayScience#117) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * software gardening of preprocessing * add preprocces step * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Onboard new data (WayScience#119) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * adding refactor * updating scripts * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Remove unwanted modules (WayScience#122) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor and remove --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Refactor featurization (WayScience#121) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (WayScience#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * add refactored featurization * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update docs/RFC-2119-Feature-Naming-Convention.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * update segmentations * update env * add new channel reader * fix HPC settings * fix reading error * fix reading error * rerun segmentations * rerun segmentations * Update 2.segment_images/README.md Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com> * Update 2.segment_images/README.md Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com> * Update environments/segmentation_env.yml Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com> * Update 2.segment_images/README.md Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com> * Update 2.segment_images/README.md Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com> * run on hPC * udpate env --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com> Co-authored-by: Gregory Way <gregory.way@gmail.com>

review-notebook-app · 2026-03-24T18:14:33Z

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gwaybio

Impressive work, great to see this refactoring - I think we're ready to go!

Note that I wasn't able to look at all of the files (see error below). Let's try to clean up the commit history (by squashing and merging and then merging with remote fork)

This reverts commit df5214a.

* running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * set up technical analysis * update gitignore * progress capture for tech analysis * tech analysis add files * add HPC version * add HPC version * fix the script * add updates * update HPC script * compute metrics for basicpy across scopes * addressing comments + refactor * Add basicpy code to test IC on 3D data (#118) * add basicpy code to test IC on 3D data * update code per PR review * Add first draft of areashape 3D figure (#114) * add first draft of areashape 3D figure * fix pathing for image * add another option + edits * final figure updates * Update docs (#124) * add mermaid * add mermaid to sphinx env * minor updates to capitalization * clarity facelift * remove workflow diagram * add mermaid to docs requirements * stabilize url * Update docs/source/overview.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * Update docs/source/overview.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * myst mds * fix redirects * remove broken link check too flimsy!! --------- Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * Remove unwanted modules (#122) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor and remove --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * update gitignore * Refactor qc module (#120) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor qc * add scripts * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Refactor featurization (#121) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * add refactored featurization * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update docs/RFC-2119-Feature-Naming-Convention.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Tests for featurization module (#128) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update gitignore * pytests * add test updates * adding tests * addressing comments and cleaning up tests --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Nucleo centric feature extraction (#131) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update gitignore * implement the nucleo_centric_approach! * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * progress capture * progress capture * updadting segmentations * addressing comments * Docs, tests, and utils refactor (#116) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update docs and tests and src * Update src/featurization_utils/sammed3d_featurizer.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments * switch to mystic * addressing comments * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Preprocess refactor (#117) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * software gardening of preprocessing * add preprocces step * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Onboard new data (#119) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * adding refactor * updating scripts * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Remove unwanted modules (#122) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor and remove --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Refactor featurization (#121) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * add refactored featurization * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update docs/RFC-2119-Feature-Naming-Convention.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * new plots * add new figures * addressing comments: * fixed ibp * fixed ibp * fixed ibp * ibp progress capture: * progress capture * progess capture * progress capture * update ibp * addressing comments * Update tables (#133) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * set up technical analysis * update gitignore * progress capture for tech analysis * tech analysis add files * add HPC version * add HPC version * fix the script * add updates * update HPC script * compute metrics for basicpy across scopes * addressing comments + refactor * Add basicpy code to test IC on 3D data (#118) * add basicpy code to test IC on 3D data * update code per PR review * Add first draft of areashape 3D figure (#114) * add first draft of areashape 3D figure * fix pathing for image * add another option + edits * final figure updates * Update docs (#124) * add mermaid * add mermaid to sphinx env * minor updates to capitalization * clarity facelift * remove workflow diagram * add mermaid to docs requirements * stabilize url * Update docs/source/overview.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * Update docs/source/overview.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * myst mds * fix redirects * remove broken link check too flimsy!! --------- Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * Remove unwanted modules (#122) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor and remove --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * update gitignore * Refactor qc module (#120) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor qc * add scripts * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Refactor featurization (#121) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * add refactored featurization * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update docs/RFC-2119-Feature-Naming-Convention.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Tests for featurization module (#128) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update gitignore * pytests * add test updates * adding tests * addressing comments and cleaning up tests --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Nucleo centric feature extraction (#131) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update gitignore * implement the nucleo_centric_approach! * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * progress capture * progress capture * updadting segmentations * addressing comments * Docs, tests, and utils refactor (#116) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update docs and tests and src * Update src/featurization_utils/sammed3d_featurizer.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments * switch to mystic * addressing comments * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Preprocess refactor (#117) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * software gardening of preprocessing * add preprocces step * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Onboard new data (#119) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * adding refactor * updating scripts * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Remove unwanted modules (#122) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor and remove --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Refactor featurization (#121) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * add refactored featurization * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update docs/RFC-2119-Feature-Naming-Convention.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * new plots * add new figures * addressing comments: * update table2 * Update figures/table2/scripts/table2.py Co-authored-by: Cameron Mattson <92554334+MattsonCam@users.noreply.github.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com> Co-authored-by: Gregory Way <gregory.way@gmail.com> Co-authored-by: Cameron Mattson <92554334+MattsonCam@users.noreply.github.com> * Featurization refactor (#135) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * set up technical analysis * update gitignore * progress capture for tech analysis * tech analysis add files * add HPC version * add HPC version * fix the script * add updates * update HPC script * compute metrics for basicpy across scopes * addressing comments + refactor * Add basicpy code to test IC on 3D data (#118) * add basicpy code to test IC on 3D data * update code per PR review * Add first draft of areashape 3D figure (#114) * add first draft of areashape 3D figure * fix pathing for image * add another option + edits * final figure updates * Update docs (#124) * add mermaid * add mermaid to sphinx env * minor updates to capitalization * clarity facelift * remove workflow diagram * add mermaid to docs requirements * stabilize url * Update docs/source/overview.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * Update docs/source/overview.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * myst mds * fix redirects * remove broken link check too flimsy!! --------- Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * Remove unwanted modules (#122) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor and remove --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * update gitignore * Refactor qc module (#120) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor qc * add scripts * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Refactor featurization (#121) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * add refactored featurization * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update docs/RFC-2119-Feature-Naming-Convention.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Tests for featurization module (#128) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update gitignore * pytests * add test updates * adding tests * addressing comments and cleaning up tests --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Nucleo centric feature extraction (#131) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update gitignore * implement the nucleo_centric_approach! * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * progress capture * progress capture * updadting segmentations * addressing comments * Docs, tests, and utils refactor (#116) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update docs and tests and src * Update src/featurization_utils/sammed3d_featurizer.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments * switch to mystic * addressing comments * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Preprocess refactor (#117) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * software gardening of preprocessing * add preprocces step * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Onboard new data (#119) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * adding refactor * updating scripts * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Remove unwanted modules (#122) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor and remove --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Refactor featurization (#121) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * add refactored featurization * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update docs/RFC-2119-Feature-Naming-Convention.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * new plots * add new figures * addressing comments: * fix featurization, fix tests, and fix profiling * changes to featurization * changes to featurization * run on HPC * add uv * adding features * adding features * new features * add features * address comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com> Co-authored-by: Gregory Way <gregory.way@gmail.com> * Segmentation optimization (#134) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * set up technical analysis * update gitignore * progress capture for tech analysis * tech analysis add files * add HPC version * add HPC version * fix the script * add updates * update HPC script * compute metrics for basicpy across scopes * addressing comments + refactor * Add basicpy code to test IC on 3D data (#118) * add basicpy code to test IC on 3D data * update code per PR review * Add first draft of areashape 3D figure (#114) * add first draft of areashape 3D figure * fix pathing for image * add another option + edits * final figure updates * Update docs (#124) * add mermaid * add mermaid to sphinx env * minor updates to capitalization * clarity facelift * remove workflow diagram * add mermaid to docs requirements * stabilize url * Update docs/source/overview.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * Update docs/source/overview.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * myst mds * fix redirects * remove broken link check too flimsy!! --------- Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * Remove unwanted modules (#122) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor and remove --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * update gitignore * Refactor qc module (#120) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * refactor qc * add scripts * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Refactor featurization (#121) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * add refactored featurization * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update 3.cellprofiling/README.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update docs/RFC-2119-Feature-Naming-Convention.md Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Tests for featurization module (#128) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update gitignore * pytests * add test updates * adding tests * addressing comments and cleaning up tests --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Nucleo centric feature extraction (#131) * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * running on HPC * push to HPC * push to HPC * push to HPC * run on HPC * rerun on HPC * push to HPC * push to HPC * running ibp * ibp * complete ibp * addressing comments * Segmentations for 3D (#106) * ready for hPC * processed all segs * rerun organoid segs on HPC * fixed HPC script * fixed HPC script * update run list * update run list * update run list * update run list * update run list * segmentations re-completed * Update 2.segment_images/scripts/0.nuclei_segmentation.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * addressing comments --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com> * precommit * update gitignore * implement the nucleo_centric_approach! * addressing comments ------…

MikeLippincott and others added 30 commits January 13, 2026 14:07

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MikeLippincott and others added 21 commits March 12, 2026 13:09

Merge remote-tracking branch 'upstream/main'

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gwaybio approved these changes Mar 24, 2026

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Merge branch 'main' into running_segmentation

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MikeLippincott merged commit df5214a into WayScience:main Mar 24, 2026
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MikeLippincott added a commit that referenced this pull request Mar 24, 2026

Revert "Running segmentation (#139)"

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Running segmentation#139

Running segmentation#139
MikeLippincott merged 104 commits intoWayScience:mainfrom
MikeLippincott:running_segmentation

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MikeLippincott commented Mar 24, 2026

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