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diagnostics
diagnostics
 
 
00_setup_paths.py
00_setup_paths.py
 
 
01_run_pipelines.py
01_run_pipelines.py
 
 
02_compare_per_cell.py
02_compare_per_cell.py
 
 
03_compare_aggregates.py
03_compare_aggregates.py
 
 
04_compare_yeast.py
04_compare_yeast.py
 
 
04_synthetic_sphericity.py
04_synthetic_sphericity.py
 
 
05_algorithmic_sanity.py
05_algorithmic_sanity.py
 
 
05_compare_mammalian_coloc.py
05_compare_mammalian_coloc.py
 
 
06_timing_report.py
06_timing_report.py
 
 
07_report.py
07_report.py
 
 
08_yeast_coloc_figure.py
08_yeast_coloc_figure.py
 
 
09_pca_3d_yeast.py
09_pca_3d_yeast.py
 
 
10_figure4_pca_umap_3d.py
10_figure4_pca_umap_3d.py
 
 
11_figure3_yeast_3d.py
11_figure3_yeast_3d.py
 
 
12_tables_s2_s3_3d.py
12_tables_s2_s3_3d.py
 
 
13_figure2_mammalian_2d.py
13_figure2_mammalian_2d.py
 
 
14_figure4_responder_modes.py
14_figure4_responder_modes.py
 
 
15_figureS1_hct116_supp.py
15_figureS1_hct116_supp.py
 
 
16_figureS2_yeast_supp.py
16_figureS2_yeast_supp.py
 
 
HANDOFF_yeast_3D.md
HANDOFF_yeast_3D.md
 
 
MAMMALIAN_COLOC_3D.md
MAMMALIAN_COLOC_3D.md
 
 
MIDWAY3_CORRECTED_RUN.md
MIDWAY3_CORRECTED_RUN.md
 
 
PCA_3D_YEAST.md
PCA_3D_YEAST.md
 
 
README.md
README.md
 
 
YEAST_COLOC_3D.md
YEAST_COLOC_3D.md
 
 
compare_erosion_2d.py
compare_erosion_2d.py
 
 
diagnose_puncta_edge.py
diagnose_puncta_edge.py
 
 
diagnose_sphericity.py
diagnose_sphericity.py
 
 
paths.local.json.example
paths.local.json.example
 
 
seg_diagnose_part1.py
seg_diagnose_part1.py
 
 
seg_diagnose_part2.py
seg_diagnose_part2.py
 
 
seg_diagnose_part3.py
seg_diagnose_part3.py
 
 
seg_exp_B1.py
seg_exp_B1.py
 
 
seg_exp_B2.py
seg_exp_B2.py
 
 
seg_exp_B2_all6.py
seg_exp_B2_all6.py
 
 
seg_exp_B3.py
seg_exp_B3.py
 
 
seg_exp_B3_all6.py
seg_exp_B3_all6.py
 
 
seg_exp_C.py
seg_exp_C.py
 
 
seg_experiments_runner.py
seg_experiments_runner.py
 
 

README.md

3D validation harness

Scripts that reproduce the 2D-vs-3D validation analysis for cellquant. Run outputs, logs, and large image data are gitignored; only the .py/.md code and this README are tracked as the reproducibility record.

Configuring the data root

Paths are resolved portably in 00_setup_paths.py — there is no hardcoded machine path, so the identical harness runs on the Mac and on Midway3. The project root (the directory containing cellquant.py, validation_3d/, and the data dirs SG_zstacks/ and Tif6_Nsr1_Sis1_6hr/) is resolved in this order:

  1. $CELLQUANT_VALIDATION_ROOT — explicit override, e.g. export CELLQUANT_VALIDATION_ROOT=/scratch/midway3/pincus/cellquant_run
  2. validation_3d/paths.local.json — copy paths.local.json.example and set project_root (this file is gitignored).
  3. Repo-relative default — the parent of validation_3d/. This already works on both machines when the data sits alongside the harness, so most setups need no configuration at all.

Resolution fails loudly (FileNotFoundError) if the resolved root does not exist or is missing cellquant.py / validation_3d/, naming the resolved path and the env var to set. Missing image data is reported separately, and loudly, when a dataset is actually listed (_glob_required).