LICENSE
MANIFEST.in
README.rst
deploy_docs.sh
environment.yaml
pyproject.toml
requirements.txt
rtd_trigger.txt
setup.py
setup_docs.sh
docs/genindex.html
docs/index.html
docs/objects.inv
docs/py-modindex.html
docs/search.html
docs/searchindex.js
docs/_images/logo_spacr.png
docs/_modules/SetupDict.html
docs/_modules/evaluate.html
docs/_modules/generate_mapping.html
docs/_modules/index.html
docs/_modules/main.html
docs/_modules/predict.html
docs/_modules/core/BasePredictor.html
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docs/_modules/core/utils.html
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docs/_modules/spacr/core.html
docs/_modules/spacr/deep_spacr.html
docs/_modules/spacr/gui.html
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docs/_modules/spacr/gui_elements.html
docs/_modules/spacr/gui_utils.html
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docs/_modules/spacr/logger.html
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docs/_modules/spacr/mediar.html
docs/_modules/spacr/ml.html
docs/_modules/spacr/plot.html
docs/_modules/spacr/sequencing.html
docs/_modules/spacr/settings.html
docs/_modules/spacr/sim.html
docs/_modules/spacr/sp_stats.html
docs/_modules/spacr/spacr_cellpose.html
docs/_modules/spacr/submodules.html
docs/_modules/spacr/timelapse.html
docs/_modules/spacr/toxo.html
docs/_modules/spacr/utils.html
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docs/_sources/api/index.rst.txt
docs/_sources/api/SetupDict/index.rst.txt
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docs/_sources/api/core/BasePredictor/index.rst.txt
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docs/_sources/api/core/MEDIAR/index.rst.txt
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spacr/__init__.py
spacr/__main__.py
spacr/_v1_v2_bridge.py
spacr/active_learning.py
spacr/agreement.py
spacr/align.py
spacr/app_annotate.py
spacr/app_classify.py
spacr/app_make_masks.py
spacr/app_mask.py
spacr/app_measure.py
spacr/app_sequencing.py
spacr/app_umap.py
spacr/attribution.py
spacr/batch.py
spacr/cli.py
spacr/cli_repro.py
spacr/convert.py
spacr/core.py
spacr/crops.py
spacr/custom_features.py
spacr/deep_spacr.py
spacr/diameter.py
spacr/errors.py
spacr/feature_dict.py
spacr/foreign.py
spacr/gui.py
spacr/gui_core.py
spacr/gui_elements.py
spacr/gui_utils.py
spacr/hyperparam.py
spacr/image_colors.py
spacr/io.py
spacr/logger.py
spacr/logging_util.py
spacr/mask_io.py
spacr/measure.py
spacr/measurement_schema.py
spacr/ml.py
spacr/model_compare.py
spacr/model_zoo.py
spacr/notebook_export.py
spacr/object.py
spacr/pipeline_v2.py
spacr/plate_qc.py
spacr/plot.py
spacr/predictions.py
spacr/report.py
spacr/resume.py
spacr/row_exclusions.py
spacr/run_journal.py
spacr/schema.py
spacr/seg_qc.py
spacr/sequencing.py
spacr/settings.py
spacr/sim.py
spacr/sp_stats.py
spacr/spacr_cellpose.py
spacr/spacrops.py
spacr/submodules.py
spacr/tiff_io.py
spacr/timelapse.py
spacr/torch_artifacts.py
spacr/toxo.py
spacr/train_compare.py
spacr/umap_annotations.py
spacr/updater.py
spacr/utils.py
spacr/validate.py
spacr/version.py
spacr/zstack.py
spacr.egg-info/PKG-INFO
spacr.egg-info/SOURCES.txt
spacr.egg-info/dependency_links.txt
spacr.egg-info/entry_points.txt
spacr.egg-info/requires.txt
spacr.egg-info/top_level.txt
spacr/qt/__init__.py
spacr/qt/__main__.py
spacr/qt/annotate_engine.py
spacr/qt/app.py
spacr/qt/bridge.py
spacr/qt/command_palette.py
spacr/qt/dnd.py
spacr/qt/dnd_handlers.py
spacr/qt/first_run.py
spacr/qt/folder_metadata.py
spacr/qt/hf_download.py
spacr/qt/iconset.py
spacr/qt/imagery.py
spacr/qt/ingest_preview.py
spacr/qt/logging_util.py
spacr/qt/mask_engine.py
spacr/qt/multi_format.py
spacr/qt/notify.py
spacr/qt/plate_queue.py
spacr/qt/preferences.py
spacr/qt/prefs.py
spacr/qt/regex_detect.py
spacr/qt/regex_editor.py
spacr/qt/settings_diff.py
spacr/qt/shortcuts.py
spacr/qt/space.py
spacr/qt/synthetic.py
spacr/qt/theme.py
spacr/qt/verbose_logger.py
spacr/qt/ai/__init__.py
spacr/qt/ai/github_auth.py
spacr/qt/ai/issue_report.py
spacr/qt/ai/keys.py
spacr/qt/ai/prompts.py
spacr/qt/ai/providers.py
spacr/qt/ai/settings.py
spacr/qt/ai/worker.py
spacr/qt/screens/__init__.py
spacr/qt/screens/agreement.py
spacr/qt/screens/align.py
spacr/qt/screens/annotate.py
spacr/qt/screens/app_screen.py
spacr/qt/screens/batch.py
spacr/qt/screens/convert.py
spacr/qt/screens/db_browser.py
spacr/qt/screens/foreign.py
spacr/qt/screens/hyperparam.py
spacr/qt/screens/make_masks.py
spacr/qt/screens/model_compare.py
spacr/qt/screens/model_zoo.py
spacr/qt/screens/plate_view.py
spacr/qt/screens/queue.py
spacr/qt/screens/report.py
spacr/qt/screens/settings_model.py
spacr/qt/screens/train_compare.py
spacr/qt/tutorial/__init__.py
spacr/qt/tutorial/__main__.py
spacr/qt/tutorial/engine.py
spacr/qt/tutorial/scripts.py
spacr/qt/widgets/__init__.py
spacr/qt/widgets/ai_chat_panel.py
spacr/qt/widgets/ai_toggle_label.py
spacr/qt/widgets/barcode_regex.py
spacr/qt/widgets/card.py
spacr/qt/widgets/column_picker.py
spacr/qt/widgets/console_panel.py
spacr/qt/widgets/divider.py
spacr/qt/widgets/dna_rain.py
spacr/qt/widgets/drawer.py
spacr/qt/widgets/eliding.py
spacr/qt/widgets/empty_state.py
spacr/qt/widgets/figure_queue.py
spacr/qt/widgets/home.py
spacr/qt/widgets/hover_tooltip.py
spacr/qt/widgets/info_link.py
spacr/qt/widgets/live_preview.py
spacr/qt/widgets/measure_preview.py
spacr/qt/widgets/metadata_table.py
spacr/qt/widgets/motility_preview.py
spacr/qt/widgets/row_exclusion.py
spacr/qt/widgets/section.py
spacr/qt/widgets/tile.py
spacr/qt/widgets/timelapse_preview.py
spacr/qt/widgets/toggle.py
spacr/qt/widgets/umap_explorer.py
spacr/qt/widgets/usage_bar.py
spacr/resources/data/barcodes_column.csv
spacr/resources/data/barcodes_grna.csv
spacr/resources/data/barcodes_row.csv
spacr/resources/data/lopit.csv
spacr/resources/data/toxoplasma_metadata.csv
spacr/resources/font/open_sans/OFL.txt
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spacr/resources/font/open_sans/OpenSans-VariableFont_wdth,wght.ttf
spacr/resources/font/open_sans/README.txt
spacr/resources/font/open_sans/static/OpenSans-Bold.ttf
spacr/resources/font/open_sans/static/OpenSans-BoldItalic.ttf
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spacr/resources/font/open_sans/static/OpenSans-SemiBoldItalic.ttf
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spacr/resources/icons/convert.png
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spacr/resources/icons/flow_chart_v3.png
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spacr/resources/icons/invasion.png
spacr/resources/icons/loading_spinner.gif
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spacr/resources/icons/logo_spacr_v1.png
spacr/resources/icons/make_masks.png
spacr/resources/icons/map_barcodes.png
spacr/resources/icons/mask.png
spacr/resources/icons/measure.png
spacr/resources/icons/ml_analyze.png
spacr/resources/icons/motility.png
spacr/resources/icons/plaque.png
spacr/resources/icons/queue.png
spacr/resources/icons/recruitment.png
spacr/resources/icons/regression.png
spacr/resources/icons/replication.png
spacr/resources/icons/run.png
spacr/resources/icons/sequencing.png
spacr/resources/icons/settings.png
spacr/resources/icons/timelapse.png
spacr/resources/icons/train_cellpose.png
spacr/resources/icons/train_compare.png
spacr/resources/icons/umap.png
spacr/resources/themes/deep_field.jpg
spacr/resources/themes/filopodia.jpg
spacr/resources/themes/microtubules.jpg
tests/test_active_learning.py
tests/test_agreement.py
tests/test_agreement_excludes_the_model.py
tests/test_align.py
tests/test_align_cov.py
tests/test_all_plotting_functions.py
tests/test_analysis_modules.py
tests/test_analysis_modules_t10.py
tests/test_analysis_submodules_real_data.py
tests/test_annotation_app.py
tests/test_app_entry_consistency.py
tests/test_app_registry_parity.py
tests/test_attribution.py
tests/test_batch.py
tests/test_cellpose4_model_story.py
tests/test_cellpose4_spacrops_submodules.py
tests/test_ci_suite_classification.py
tests/test_class_imbalance.py
tests/test_cleanup_pipeline_folders.py
tests/test_cli.py
tests/test_cli_repro_and_diff.py
tests/test_column_name_canonicalization.py
tests/test_conda_forge_recipe.py
tests/test_console_encoding.py
tests/test_convert.py
tests/test_convert_1536.py
tests/test_core_branches.py
tests/test_core_edge_branches.py
tests/test_core_mask_orchestration.py
tests/test_core_umap_graphs.py
tests/test_core_umap_validation.py
tests/test_cov_deep_spacr_activation_maps.py
tests/test_cov_deep_spacr_apply_model.py
tests/test_cov_deep_spacr_entry_fusion.py
tests/test_cov_deep_spacr_metrics.py
tests/test_cov_deep_spacr_smoothgrad_examples.py
tests/test_cov_deep_spacr_train_model.py
tests/test_cov_deep_spacr_train_test_entry.py
tests/test_cov_gui_elements_annotate_db.py
tests/test_cov_gui_elements_annotate_deep.py
tests/test_cov_gui_elements_annotate_image.py
tests/test_cov_gui_elements_figure_tools.py
tests/test_cov_gui_elements_modify_mask_app.py
tests/test_cov_gui_elements_widgets_basic.py
tests/test_cov_gui_elements_widgets_card_toggle.py
tests/test_cov_gui_elements_widgets_progress.py
tests/test_cov_io_datasets.py
tests/test_cov_io_db_arrays.py
tests/test_cov_io_loaders_images.py
tests/test_cov_io_merge_mip.py
tests/test_cov_io_normalize.py
tests/test_cov_io_organize_files.py
tests/test_cov_io_preprocess_entry.py
tests/test_cov_io_stack_norm.py
tests/test_cov_io_tail.py
tests/test_cov_ml_ml_scores.py
tests/test_cov_ml_perform_regression.py
tests/test_cov_ml_reads_scores.py
tests/test_cov_ml_regression_core.py
tests/test_cov_ml_shap_vision.py
tests/test_cov_ml_simulation.py
tests/test_cov_ml_stats_prep.py
tests/test_cov_object_cellpose_masks.py
tests/test_cov_object_classical_spots.py
tests/test_cov_object_masks_sam.py
tests/test_cov_object_merge_split.py
tests/test_cov_object_network_ring.py
tests/test_cov_object_organelle_sam.py
tests/test_cov_object_preprocess_segment.py
tests/test_cov_plot_arrays_browse.py
tests/test_cov_plot_cellpose_output.py
tests/test_cov_plot_compare_viz.py
tests/test_cov_plot_db_csv_region.py
tests/test_cov_plot_grouped_graph.py
tests/test_cov_plot_importance_volcano.py
tests/test_cov_plot_merged_grid.py
tests/test_cov_plot_overlay_core.py
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tests/test_cov_submodules_recruitment_plaques.py
tests/test_cov_submodules_vision_model.py
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tests/test_cov_timelapse_movies_gifs.py
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tests/test_cov_utils_cleanup_paths.py
tests/test_cov_utils_crop_recruitment.py
tests/test_cov_utils_feature_stats.py
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tests/test_crop_source_wiring.py
tests/test_crops.py
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tests/test_db_contract_cell_id.py
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tests/test_io_datasets_convert.py
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