LICENSE
MANIFEST.in
README.md
pyproject.toml
src/PyMicroglia.egg-info/PKG-INFO
src/PyMicroglia.egg-info/SOURCES.txt
src/PyMicroglia.egg-info/dependency_links.txt
src/PyMicroglia.egg-info/entry_points.txt
src/PyMicroglia.egg-info/requires.txt
src/PyMicroglia.egg-info/top_level.txt
src/pymicroglia/__init__.py
src/pymicroglia/_optional.py
src/pymicroglia/_outlines.py
src/pymicroglia/_results.py
src/pymicroglia/_sources.py
src/pymicroglia/catalogue.py
src/pymicroglia/cli.py
src/pymicroglia/config.py
src/pymicroglia/context.py
src/pymicroglia/controls.py
src/pymicroglia/display.py
src/pymicroglia/eligibility.py
src/pymicroglia/filtering.py
src/pymicroglia/guards.py
src/pymicroglia/imagej.py
src/pymicroglia/io.py
src/pymicroglia/knowledge.py
src/pymicroglia/metadata.py
src/pymicroglia/params.py
src/pymicroglia/publication.py
src/pymicroglia/pymicroglia_context.json
src/pymicroglia/qc.py
src/pymicroglia/recording.py
src/pymicroglia/registration.py
src/pymicroglia/registry.py
src/pymicroglia/results.py
src/pymicroglia/review.py
src/pymicroglia/rhythm.py
src/pymicroglia/roi.py
src/pymicroglia/run.py
src/pymicroglia/scn_outline.py
src/pymicroglia/segmentation.py
src/pymicroglia/series.py
src/pymicroglia/trace_tables.py
src/pymicroglia/tracing.py
src/pymicroglia/workbench.py
src/pymicroglia/_workbench/__init__.py
src/pymicroglia/_workbench/descriptive.py
src/pymicroglia/_workbench/estimates.py
src/pymicroglia/_workbench/options.py
src/pymicroglia/_workbench/processing.py
src/pymicroglia/clustering/__init__.py
src/pymicroglia/clustering/cohort.py
src/pymicroglia/clustering/fingerprint.py
src/pymicroglia/clustering/options.py
src/pymicroglia/cosmic/__init__.py
src/pymicroglia/data/actions.json
src/pymicroglia/data/behaviour-states.example.json
src/pymicroglia/data/clustering-options.example.json
src/pymicroglia/data/clustering.example.json
src/pymicroglia/data/figure_options.json
src/pymicroglia/data/intervention-response.example.json
src/pymicroglia/data/relationships.example.json
src/pymicroglia/data/spatial-coordination.example.json
src/pymicroglia/data/states.example.json
src/pymicroglia/figure_tables/__init__.py
src/pymicroglia/figure_tables/actions.py
src/pymicroglia/figure_tables/agreement_display.py
src/pymicroglia/figure_tables/aligned_clocks.py
src/pymicroglia/figure_tables/all_cell_traces.py
src/pymicroglia/figure_tables/audit_display.py
src/pymicroglia/figure_tables/audit_focused.py
src/pymicroglia/figure_tables/audit_saved.py
src/pymicroglia/figure_tables/cell_review.py
src/pymicroglia/figure_tables/changes.py
src/pymicroglia/figure_tables/clock_face.py
src/pymicroglia/figure_tables/connection_display.py
src/pymicroglia/figure_tables/contacts.py
src/pymicroglia/figure_tables/contrast.py
src/pymicroglia/figure_tables/coordination_display.py
src/pymicroglia/figure_tables/coverage.py
src/pymicroglia/figure_tables/cycle_repeatability.py
src/pymicroglia/figure_tables/daily_profiles.py
src/pymicroglia/figure_tables/distributions.py
src/pymicroglia/figure_tables/event_labels.py
src/pymicroglia/figure_tables/exchange.py
src/pymicroglia/figure_tables/export_options.py
src/pymicroglia/figure_tables/film_action.py
src/pymicroglia/figure_tables/focused_display.py
src/pymicroglia/figure_tables/follow.py
src/pymicroglia/figure_tables/group_display.py
src/pymicroglia/figure_tables/images.py
src/pymicroglia/figure_tables/independence.py
src/pymicroglia/figure_tables/intervention_display.py
src/pymicroglia/figure_tables/intervention_report_display.py
src/pymicroglia/figure_tables/lag_display.py
src/pymicroglia/figure_tables/lag_profiles.py
src/pymicroglia/figure_tables/lifecycle.py
src/pymicroglia/figure_tables/method_audit.py
src/pymicroglia/figure_tables/metric_maps.py
src/pymicroglia/figure_tables/metric_matrix.py
src/pymicroglia/figure_tables/motility.py
src/pymicroglia/figure_tables/null_channels.py
src/pymicroglia/figure_tables/ordering.py
src/pymicroglia/figure_tables/page_views.py
src/pymicroglia/figure_tables/pair_card_display.py
src/pymicroglia/figure_tables/patches.py
src/pymicroglia/figure_tables/pipeline_inputs.py
src/pymicroglia/figure_tables/pixel_fates.py
src/pymicroglia/figure_tables/plans.py
src/pymicroglia/figure_tables/population_display.py
src/pymicroglia/figure_tables/predictability.py
src/pymicroglia/figure_tables/prepared.py
src/pymicroglia/figure_tables/presence.py
src/pymicroglia/figure_tables/programmes.py
src/pymicroglia/figure_tables/radial.py
src/pymicroglia/figure_tables/radial_rhythms.py
src/pymicroglia/figure_tables/recurrence.py
src/pymicroglia/figure_tables/regime_reporter.py
src/pymicroglia/figure_tables/regimes.py
src/pymicroglia/figure_tables/relationship_matrix_display.py
src/pymicroglia/figure_tables/relationship_report_display.py
src/pymicroglia/figure_tables/report_card.py
src/pymicroglia/figure_tables/reporter_rhythms.py
src/pymicroglia/figure_tables/rhythm_eligibility.py
src/pymicroglia/figure_tables/rhythm_processing.py
src/pymicroglia/figure_tables/rhythm_saved.py
src/pymicroglia/figure_tables/rhythm_traces.py
src/pymicroglia/figure_tables/saved.py
src/pymicroglia/figure_tables/screen_overview.py
src/pymicroglia/figure_tables/spatial.py
src/pymicroglia/figure_tables/spatial_views.py
src/pymicroglia/figure_tables/state_card_display.py
src/pymicroglia/figure_tables/state_profile_display.py
src/pymicroglia/figure_tables/state_review.py
src/pymicroglia/figure_tables/state_summary_display.py
src/pymicroglia/figure_tables/territory_values.py
src/pymicroglia/figure_tables/time_matrix.py
src/pymicroglia/figure_tables/timeline_display.py
src/pymicroglia/figure_tables/timing_display.py
src/pymicroglia/figure_tables/tissue.py
src/pymicroglia/figure_tables/tissue_rhythms.py
src/pymicroglia/figure_tables/trace_display.py
src/pymicroglia/figure_tables/traits.py
src/pymicroglia/figure_tables/trajectories.py
src/pymicroglia/figure_tables/triggered.py
src/pymicroglia/figure_tables/upheaval.py
src/pymicroglia/guide/clustering.md
src/pymicroglia/guide/figures.md
src/pymicroglia/guide/inputs.md
src/pymicroglia/guide/lifecycle.md
src/pymicroglia/guide/measure.md
src/pymicroglia/guide/overview.md
src/pymicroglia/guide/pipelines.md
src/pymicroglia/guide/quickstart.md
src/pymicroglia/guide/records.md
src/pymicroglia/guide/rhythms.md
src/pymicroglia/guide/states.md
src/pymicroglia/guide/tracking.md
src/pymicroglia/guide/troubleshooting.md
src/pymicroglia/learned_mask/__init__.py
src/pymicroglia/learned_mask/apply.py
src/pymicroglia/learned_mask/filters.py
src/pymicroglia/learned_mask/network.py
src/pymicroglia/learned_mask/refine.py
src/pymicroglia/learned_mask/scale.py
src/pymicroglia/measure/__init__.py
src/pymicroglia/measure/behaviour_sample_statistics.py
src/pymicroglia/measure/conditions.py
src/pymicroglia/measure/context.py
src/pymicroglia/measure/contrast_statistics.py
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src/pymicroglia/measure/coordination_statistics.py
src/pymicroglia/measure/declare.py
src/pymicroglia/measure/defaults.py
src/pymicroglia/measure/fields.py
src/pymicroglia/measure/gaps.py
src/pymicroglia/measure/inputs.py
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src/pymicroglia/measure/modules/channels.py
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src/pymicroglia/measure/modules/objects.py
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src/pymicroglia/measure/modules/regimes.py
src/pymicroglia/measure/modules/rhythms.py
src/pymicroglia/measure/modules/sequence_distance.py
src/pymicroglia/measure/modules/sholl.py
src/pymicroglia/measure/modules/surveillance.py
src/pymicroglia/measure/modules/territory.py
src/pymicroglia/measure/modules/territory_shape.py
src/pymicroglia/measure/modules/trend.py
src/pymicroglia/measure/modules/walk.py
src/pymicroglia/pipelines/__init__.py
src/pymicroglia/pipelines/_auto_microglia_support.py
src/pymicroglia/pipelines/_contracts.py
src/pymicroglia/pipelines/_records.py
src/pymicroglia/pipelines/_requests.py
src/pymicroglia/pipelines/_runner.py
src/pymicroglia/pipelines/_saved_figures.py
src/pymicroglia/pipelines/_screening.py
src/pymicroglia/pipelines/_tables.py
src/pymicroglia/pipelines/_versions.py
src/pymicroglia/pipelines/auto_microglia.py
src/pymicroglia/pipelines/behaviour_states.py
src/pymicroglia/pipelines/bioluminescence.py
src/pymicroglia/pipelines/cell_masks.py
src/pymicroglia/pipelines/cry1_dluc_photon.py
src/pymicroglia/pipelines/dluc_single_cell.py
src/pymicroglia/pipelines/intervention_response.py
src/pymicroglia/pipelines/measurement_relationships.py
src/pymicroglia/pipelines/method_audit.py
src/pymicroglia/pipelines/motion_handoff.py
src/pymicroglia/pipelines/objects.py
src/pymicroglia/pipelines/phase_green_red.py
src/pymicroglia/pipelines/registered.py
src/pymicroglia/pipelines/request_contracts.py
src/pymicroglia/pipelines/rhythm_discovery.py
src/pymicroglia/pipelines/spatial_coordination.py
src/pymicroglia/pipelines/audit/__init__.py
src/pymicroglia/pipelines/audit/benchmarks.py
src/pymicroglia/pipelines/audit/confirmation.py
src/pymicroglia/pipelines/audit/evaluator.py
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src/pymicroglia/pipelines/audit/focus.py
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src/pymicroglia/pipelines/audit/profiles.py
src/pymicroglia/pipelines/audit/scoring.py
src/pymicroglia/pipelines/audit/selection.py
src/pymicroglia/pipelines/audit/stability.py
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src/pymicroglia/pipelines/behaviour/__init__.py
src/pymicroglia/pipelines/behaviour/assignments.py
src/pymicroglia/pipelines/behaviour/candidates.py
src/pymicroglia/pipelines/behaviour/card_figures.py
src/pymicroglia/pipelines/behaviour/card_images.py
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src/pymicroglia/pipelines/behaviour/summary_figures.py
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src/pymicroglia/states/behaviour_models.py
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src/pymicroglia/states/demo.py
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src/pymicroglia/states/rhythms.py
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src/pymicroglia/visualisation/panels/rhythm_audit.py
src/pymicroglia/visualisation/panels/rhythm_evidence.py
src/pymicroglia/visualisation/panels/rhythm_groups.py
src/pymicroglia/visualisation/panels/rhythm_overview.py
src/pymicroglia/visualisation/panels/rhythm_relationships.py
src/pymicroglia/visualisation/panels/rhythm_time_matrix.py
src/pymicroglia/visualisation/panels/rhythm_timing.py
src/pymicroglia/visualisation/panels/saved.py
src/pymicroglia/visualisation/panels/spatial.py
src/pymicroglia/visualisation/panels/spatial_views.py
src/pymicroglia/visualisation/panels/state_review.py
src/pymicroglia/visualisation/panels/tissue.py
src/pymicroglia/visualisation/panels/traits.py
src/pymicroglia/visualisation/panels/trajectories.py
src/pymicroglia/visualisation/panels/triggered.py
src/pymicroglia/visualisation/panels/upheaval.py
src/pymicroglia/visualisation/panels/wording.py