AGENTS.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
src/Auto_Organotypic.egg-info/PKG-INFO
src/Auto_Organotypic.egg-info/SOURCES.txt
src/Auto_Organotypic.egg-info/dependency_links.txt
src/Auto_Organotypic.egg-info/entry_points.txt
src/Auto_Organotypic.egg-info/requires.txt
src/Auto_Organotypic.egg-info/top_level.txt
src/auto_organotypic/__init__.py
src/auto_organotypic/__main__.py
src/auto_organotypic/baselines.py
src/auto_organotypic/batch.py
src/auto_organotypic/broad_crop.py
src/auto_organotypic/cellgrid.py
src/auto_organotypic/chain.py
src/auto_organotypic/config.py
src/auto_organotypic/corrections.py
src/auto_organotypic/desktop.py
src/auto_organotypic/display.py
src/auto_organotypic/fiji.py
src/auto_organotypic/filtering.py
src/auto_organotypic/follow.py
src/auto_organotypic/grid.py
src/auto_organotypic/guards.py
src/auto_organotypic/hand_drawn.py
src/auto_organotypic/image.py
src/auto_organotypic/instrumental.py
src/auto_organotypic/io.py
src/auto_organotypic/launcher.py
src/auto_organotypic/layout.py
src/auto_organotypic/metadata.py
src/auto_organotypic/orientation.py
src/auto_organotypic/pipeline.py
src/auto_organotypic/qc.py
src/auto_organotypic/region_trace.py
src/auto_organotypic/registration.py
src/auto_organotypic/review.py
src/auto_organotypic/rhythm.py
src/auto_organotypic/roi.py
src/auto_organotypic/schedule.py
src/auto_organotypic/series.py
src/auto_organotypic/server.py
src/auto_organotypic/sources.py
src/auto_organotypic/split.py
src/auto_organotypic/staleness.py
src/auto_organotypic/timebase.py
src/auto_organotypic/tissue.py
src/auto_organotypic/trace_plot.py
src/auto_organotypic/trim.py
src/auto_organotypic/video_grid.py
src/auto_organotypic/windows.py
src/auto_organotypic/cosmic/__init__.py
src/auto_organotypic/cosmic/clean.py
src/auto_organotypic/cosmic/output.py
src/auto_organotypic/cosmic/rule.py
src/auto_organotypic/cosmic/stack.py
src/auto_organotypic/macros/1_rotate_expand_stack.ijm
src/auto_organotypic/macros/2_extract_hemislices.ijm
src/auto_organotypic/macros/3_define_roi.ijm
src/auto_organotypic/macros/4_extract_cellgrid.ijm
src/auto_organotypic/outline/__init__.py
src/auto_organotypic/outline/carve.py
src/auto_organotypic/outline/crop.py
src/auto_organotypic/outline/draw.py
src/auto_organotypic/outline/metrics.py
src/auto_organotypic/outline/midline.py
src/auto_organotypic/outline/planes.py
src/auto_organotypic/outline/region.py
src/auto_organotypic/outline/report.py
src/auto_organotypic/outline/run.py
src/auto_organotypic/outline/smoothing.py
src/auto_organotypic/render/__init__.py
src/auto_organotypic/render/annotate.py
src/auto_organotypic/render/channels.py
src/auto_organotypic/render/frames.py
src/auto_organotypic/render/looks.py
src/auto_organotypic/render/luts.py
src/auto_organotypic/render/outlines.py
src/auto_organotypic/render/plan.py
src/auto_organotypic/render/record.py
src/auto_organotypic/render/screen.py
src/auto_organotypic/render/tiles.py
src/auto_organotypic/static/app.js
src/auto_organotypic/static/index.html
src/auto_organotypic/static/styles.css
src/auto_organotypic/store/__init__.py
src/auto_organotypic/store/budget.py
src/auto_organotypic/store/keys.py
src/auto_organotypic/store/manifest.py
src/auto_organotypic/store/tier_a.py
src/auto_organotypic/store/tier_b.py
src/auto_organotypic/superseded/__init__.py
src/auto_organotypic/superseded/matched_line.py
src/auto_organotypic/video/__init__.py
src/auto_organotypic/video/encode.py
src/auto_organotypic/video/exports.py
tests/conftest.py
tests/test_artefact_looks.py
tests/test_automatic_scn_outline_parity.py
tests/test_batch_scn_outline.py
tests/test_broad_crop.py
tests/test_cellgrid.py
tests/test_cellgrid_parity.py
tests/test_command_line.py
tests/test_corrections.py
tests/test_cosmic_rule.py
tests/test_day_sheet.py
tests/test_desktop.py
tests/test_display_gamma.py
tests/test_drift_free_video.py
tests/test_follow.py
tests/test_given_geometry.py
tests/test_grid_export.py
tests/test_hand_drawn.py
tests/test_image_export.py
tests/test_layout.py
tests/test_outline_overlay.py
tests/test_package.py
tests/test_picture_cli.py
tests/test_pipeline.py
tests/test_pipeline_pictures.py
tests/test_region_population.py
tests/test_region_trace.py
tests/test_register_methods.py
tests/test_review.py
tests/test_rhythm_phase.py
tests/test_rhythm_public_api.py
tests/test_schedule.py
tests/test_self_contained.py
tests/test_server.py
tests/test_sources.py
tests/test_split.py
tests/test_staleness.py
tests/test_store_index.py
tests/test_store_location.py
tests/test_timebase.py
tests/test_trace_plot.py
tests/test_trim.py
tests/test_video_cli.py
tests/test_video_export.py
tests/test_video_filters.py
tests/test_video_geometry.py
tests/test_video_grid.py
tests/test_video_grid_cli.py
tests/test_windows.py
tests/evidence/parity-evidence.zip