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… scaling to extraction - Add 7 new columns from length_normed_df_more_02122026.csv (hyperparameter gaussian_sigma0p1_k100): imp_ML/DV/AP_gaussian_sigma0p1_k100 and 4 pseudocluster columns - Scale imp_ML/DV/AP (both old and new) by ×25 (voxel→µm) during extraction in sequencing.py - Remove on-the-fly ×25 scaling from main_imputation.py Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…tion - Add _IMP_PANELS registry listing all 7 imputation columns (old + new) - Add _scatter_imp generic helper to avoid repetition - Update main_imputation to a 2×4 grid showing all panels - imputed_scRNAseq and imputed_MERFISH now delegate to _scatter_imp Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ISH row 2, square subplots Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- __init__.py: add IN_CODEOCEAN flag; branch RAW/MORPHOLOGY/RESULTS_DIRECTORY to /data/LCNE-patchseq-ephys and /results when running in CodeOcean - metadata.py: import IN_CODEOCEAN/RESULTS_DIRECTORY; read cell_level_stats.csv from /results/cell_stats/ instead of S3 when IN_CODEOCEAN is set - pipeline.py: add mode banner in __main__ showing CodeOcean vs S3/local paths Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add CodeOcean end-to-end pipeline reproduction section - Add df_meta loading guide with column groups and CodeOcean behaviour - Add main figures section with entry points - Add Panel app live link and GitHub repo - Remove Installation and Contributing sections Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add tqdm to base dependencies - Remove stale panel, pipeline, and all optional-dependency groups Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
In CodeOcean mode, load_ephys_metadata(if_from_s3=True) now checks for /results/cell_stats/cell_level_stats.csv first and only falls back to S3 if the file does not exist, allowing figures to run standalone or after the eFEL pipeline in the same capsule run. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
0 (default): generate main figures only 1: run eFEL pipeline first, then generate main figures Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add CO_DATA_DIRECTORY and local-first logic to all get_public_* functions. When IN_CODEOCEAN is set, each function checks /data/LCNE-patchseq-ephys/ before falling back to S3: - get_public_efel_cell_level_stats → efel/cell_stats/cell_level_stats.csv - get_public_representative_spikes → efel/cell_stats/cell_level_*.pkl - get_public_seq_preselected → seq/seq_preselected.csv - get_public_mapmycells → seq/mapmycells_*.csv - get_public_morphology → morphology/LC_patchseq_RawFeatureWide.csv Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add paper-oriented intro, Resources table (incl. upstream ipfx/snakemake repos), and scope note - Add "Reproducing our work in Code Ocean" and "Reproducing standalone" sections - Add "Two modes of running the pipeline" comparison table - Simplify Overview and Detailed workflow with scope clarification (green arrows only) - Replace verbose eFEL pipeline/metadata sections with clean code snippet Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- isort: reorder import in figures/cached/main_figure.py - F811: remove duplicate RESULTS_DIRECTORY import in efel/pipeline.py - E501: wrap long lines in main_imputation.py, main_pca_tau.py, util.py, sequencing.py Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- noqa C901 on load_ephys_metadata and generate_violin_plot - README: warn that --rerun_efel_pipeline takes several hours Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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