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.gitignore
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# pycache
**/__pycache__/
**.pyc
# raw data but keep the metadata
data/2023*
data/objects_db
environments/SAM2_install/segment-anything-2
data/models
# logs
**.log
# cytomining logs
**runinfo
# ignore irrelevant SAM 2 outputsdata/objects_db
############################################
# IC logs
2.cellprofiler_ic_processing/notebooks/logs/
2.cellprofiler_ic_processing/scripts/logs/
2.cellprofiler_ic_processing/illum_directory
2.cellprofiler_ic_processing/illum_directory_test_small
2.cellprofiler_ic_processing/illum_directory_test
# cellprofiler logs
4.cellprofiler_analysis/scripts/logs
4.cellprofiler_analysis/scripts/*.log
4.cellprofiler_analysis/notebooks/logs
4.cellprofiler_analysis/notebooks/*.logs
# analysis results
4.cellprofiler_analysis/analysis_output
4.cellprofiler_analysis/pipelines/generated_pipelines
3a.optimizing_CP_attempt_optional/CellProfiler_optuna_utils/__pycache__
3a.optimizing_CP_attempt_optional/analysis_output/optimized_pipes
3a.optimizing_CP_attempt_optional/analysis_output/study_dir/*
3a.optimizing_CP_attempt_optional/notebooks/logs
3a.optimizing_CP_attempt_optional/scripts/logs
3a.optimizing_CP_attempt_optional/logs
3a.optimizing_CP_attempt_optional/analysis_output/
3a.optimizing_CP_attempt_optional/notebooks/runinfo
3a.optimizing_CP_attempt_optional/notebooks/optuna_profiling_utils.log
3a.optimizing_CP_attempt_optional/pipelines/generated_pipelines
3b.run_sam/memory_snapshots/
3b.run_sam/sam2_processing_dir/tiffs
3b.run_sam/sam2_processing_dir/CP_input
3b.run_sam/sam2_processing_dir/masks
3b.run_sam/sam2_processing_dir/pngs
3b.run_sam/notebooks/masks/masks.csv
3b.run_sam/masks/*.png
3b.run_sam/masks/*.csv
3b.run_sam/notebooks/videos
3b.run_sam/sam2_processing_dir/*
# cytomining results
5.process_CP_features/data/
# scDINO outputs
6.scDINO_analysis/1.scDINO_run/outputdir
# scDINO logs
6.scDINO_analysis/1.scDINO_run/.snakemake
6.scDINO_analysis/1.scDINO_run/logs
# temporal shiny app
6.scDINO_analysis/2.scDINO_processing/temporal_shiny_app
6.scDINO_analysis/2.scDINO_processing/notebooks/4.deploy_shiny_app.ipynb
6.scDINO_analysis/2.scDINO_processing/scripts/4.deploy_shiny_app.r
6.scDINO_analysis/2.scDINO_processing/temporal_shiny_app/rsconnect
# data harmonization
7.data_harmonization/data/
# data (processed)
data/models/dino_deitsmall16_pretrain_full_checkpoint.pth
data/processed_images/**
# Cluster files
*alpine_std_out_std_err-*