Adding animations by MikeLippincott · Pull Request #141 · WayScience/NF1_3D_organoid_profiling_pipeline

MikeLippincott · 2026-03-24T20:29:46Z

This PR adds the animations into the PR for use in the documentation

* 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>

* 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 ------…

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MikeLippincott · 2026-03-24T20:33:21Z

Just adding in animations here - merging in.

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

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MikeLippincott and others added 26 commits March 1, 2026 16:07

Merge remote-tracking branch 'upstream/main'

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adding the new animations

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MikeLippincott merged commit 4b509f7 into WayScience:main Mar 24, 2026
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Adding animations#141

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MikeLippincott merged 97 commits intoWayScience:mainfrom
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MikeLippincott commented Mar 24, 2026

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