README.md
setup.cfg
setup.py
luna/pathology/__init__.py
luna/pathology/analysis/__init__.py
luna/pathology/analysis/ml.py
luna/pathology/cli/__init__.py
luna/pathology/cli/dsa_annotation_etl.py
luna/pathology/cli/dsa_upload.py
luna/pathology/cli/dsa_viz.py
luna/pathology/cli/extract_kfunction_statistics.py
luna/pathology/cli/extract_shape_features.py
luna/pathology/cli/extract_stain_texture.py
luna/pathology/cli/extract_tile_statistics.py
luna/pathology/cli/generate_mask.py
luna/pathology/cli/generate_tile_labels.py
luna/pathology/cli/generate_tile_mask.py
luna/pathology/cli/generate_tiles.py
luna/pathology/cli/infer_tile_labels.py
luna/pathology/cli/run_stardist_cell_detection.py
luna/pathology/cli/run_tissue_detection.py
luna/pathology/cli/save_tiles.py
luna/pathology/cli/slide_etl.py
luna/pathology/cli/train_tissue_classifier.py
luna/pathology/cli/visualize_tile_labels_png.py
luna/pathology/cli/examples/example_bitmask_polygon_config.yaml
luna/pathology/cli/examples/example_bmp_polygon_config.yml
luna/pathology/cli/examples/example_dsa_upload_config.yaml
luna/pathology/cli/examples/example_heatmap_config.yaml
luna/pathology/cli/examples/example_qupath_polygon_config.yaml
luna/pathology/cli/examples/example_regional_polygon_config.yaml
luna/pathology/cli/examples/example_stardist_cell_config.yaml
luna/pathology/cli/examples/example_stardist_polygon_config.yaml
luna/pathology/cli/examples/generate_tile_labels_no_labels.yaml
luna/pathology/cli/examples/generate_tile_labels_with_ov_labels.yaml
luna/pathology/cli/examples/visualize_model_inference.yaml
luna/pathology/common/EnsureByteContext.py
luna/pathology/common/__init__.py
luna/pathology/common/annotation_utils.py
luna/pathology/common/build_geojson.py
luna/pathology/common/schemas.py
luna/pathology/common/slideviewer_client.py
luna/pathology/common/utils.py
luna/pathology/dsa/__init__.py
luna/pathology/dsa/dsa_api_handler.py
luna/pathology/dsa/utils.py
luna/pathology/examples/extract_feature_vectors.py
luna/pathology/slideviewer/__init__.py
luna/pathology/slideviewer/point_annotation/__init__.py
luna/pathology/slideviewer/point_annotation/proxy_table/__init__.py
luna/pathology/slideviewer/point_annotation/proxy_table/generate.py
luna/pathology/slideviewer/point_annotation/refined_table/__init__.py
luna/pathology/slideviewer/point_annotation/refined_table/generate.py
luna/pathology/slideviewer/regional_annotation/__init__.py
luna/pathology/slideviewer/regional_annotation/dask_generate.py
luna/pathology/spatial/__init__.py
luna/pathology/spatial/stats.py
luna/pathology/spatial/transforms.py
pyluna_pathology.egg-info/PKG-INFO
pyluna_pathology.egg-info/SOURCES.txt
pyluna_pathology.egg-info/dependency_links.txt
pyluna_pathology.egg-info/entry_points.txt
pyluna_pathology.egg-info/requires.txt
pyluna_pathology.egg-info/top_level.txt
pyluna_pathology.egg-info/zip-safe
tests/__init__.py
tests/test_config.yml
tests/luna/__init__.py
tests/luna/pathology/__init__.py
tests/luna/pathology/test_regional_etl_config.yaml
tests/luna/pathology/analysis/test_ml.py
tests/luna/pathology/cli/__init__.py
tests/luna/pathology/cli/test_dsa_annotation_etl.py
tests/luna/pathology/cli/test_dsa_upload.py
tests/luna/pathology/cli/test_dsa_viz.py
tests/luna/pathology/cli/test_extract_kfunction_statistics.py
tests/luna/pathology/cli/test_extract_shape_features.py
tests/luna/pathology/cli/test_extract_stain_texture.py
tests/luna/pathology/cli/test_extract_tile_statistics.py
tests/luna/pathology/cli/test_generate_mask.py
tests/luna/pathology/cli/test_generate_tile_labels.py
tests/luna/pathology/cli/test_generate_tile_mask.py
tests/luna/pathology/cli/test_generate_tiles.py
tests/luna/pathology/cli/test_infer_tile_labels.py
tests/luna/pathology/cli/test_run_stardist_cell_detection.py
tests/luna/pathology/cli/test_run_tissue_detection.py
tests/luna/pathology/cli/test_save_tiles.py
tests/luna/pathology/cli/test_slide_etl.py
tests/luna/pathology/cli/test_visualize_tile_labels_png.py
tests/luna/pathology/cli/testdata/bitmask_polygon.yml
tests/luna/pathology/cli/testdata/bitmask_polygon_upload.yml
tests/luna/pathology/cli/testdata/dsa_upload.yml
tests/luna/pathology/cli/testdata/generate_tile_labels_no_labels.yml
tests/luna/pathology/cli/testdata/generate_tile_labels_with_ov_labels.yml
tests/luna/pathology/cli/testdata/heatmap_config.yml
tests/luna/pathology/cli/testdata/qupath_polygon.yml
tests/luna/pathology/cli/testdata/regional_annotation.json
tests/luna/pathology/cli/testdata/regional_polygon.yml
tests/luna/pathology/cli/testdata/stardist_cell.yml
tests/luna/pathology/cli/testdata/stardist_polygon.yml
tests/luna/pathology/cli/testdata/test_config.yml
tests/luna/pathology/cli/testdata/test_tile_stats.parquet
tests/luna/pathology/cli/testdata/visualize_model_inference.yml
tests/luna/pathology/cli/testdata/data/dsa_annots/metadata.yml
tests/luna/pathology/cli/testdata/data/dsa_annots/slide_annotation_dataset_lung-project_Tissue-clf.parquet
tests/luna/pathology/cli/testdata/data/generate_mask/metadata.yml
tests/luna/pathology/cli/testdata/data/generate_tile_mask/metadata.yml
tests/luna/pathology/cli/testdata/data/generate_tiles/123/123.tiles.parquet
tests/luna/pathology/cli/testdata/data/generate_tiles/123/metadata.yml
tests/luna/pathology/cli/testdata/data/infer_tumor_background/123/metadata.yml
tests/luna/pathology/cli/testdata/data/infer_tumor_background/123/tile_scores_and_labels_pytorch_inference.parquet
tests/luna/pathology/cli/testdata/data/otsu_tiles/123/metadata.yml
tests/luna/pathology/cli/testdata/data/save_tiles/123/123.tiles.parquet
tests/luna/pathology/cli/testdata/data/save_tiles/123/metadata.yml
tests/luna/pathology/cli/testdata/data/stardist_cell_detection/123_cell_objects.parquet
tests/luna/pathology/cli/testdata/data/stardist_cell_detection/metadata.yml
tests/luna/pathology/cli/testdata/data/test-project/tables/WSI_patientId/part-00000-29cf1803-9c4d-4808-a0eb-03921623f806-c000.snappy.parquet
tests/luna/pathology/cli/testdata/data/test-project/tables/WSI_patientId/part-00005-e44cb98b-a9be-49c1-8c69-27b8fadcdc49-c000.snappy.parquet
tests/luna/pathology/cli/testdata/data/test-project/tables/WSI_patientId/_delta_log/00000000000000000000.json
tests/luna/pathology/cli/testdata/data/test/slides/123/test_generate_tile_ov_labels/TileScores/data/metadata.json
tests/luna/pathology/cli/testdata/data/testhub/hubconf.py
tests/luna/pathology/cli/testouts/Tile-Based_Pixel_Classifier_Inference_123.json
tests/luna/pathology/common/__init__.py
tests/luna/pathology/common/test_annotation_utils.py
tests/luna/pathology/common/test_build_geojson.py
tests/luna/pathology/common/test_slideviewer_client.py
tests/luna/pathology/common/test_utils.py
tests/luna/pathology/common/testdata/data_config_with_slideviewer_csv.yaml
tests/luna/pathology/common/testdata/data_config_without_slideviewer_csv.yaml
tests/luna/pathology/common/testdata/point_geojson_config.yaml
tests/luna/pathology/common/testdata/project/slides/123/user/RegionalAnnotationBitmap/data/123_user_SVBMP-01c9ea8d50971412600b83d4918d3888818b77792f4c40a66861bbd586ae5d51_annot.npy
tests/luna/pathology/common/testdata/project/tables/REGIONAL_METADATA_RESULTS/part-00000-91637ab6-2a29-4c77-8168-0c0ed5af3d18-c000.snappy.parquet
tests/luna/pathology/common/testdata/project/tables/REGIONAL_METADATA_RESULTS/part-00005-4bfc2771-8f4c-47c7-9271-edc0b8a4feef-c000.snappy.parquet
tests/luna/pathology/common/testdata/project/tables/REGIONAL_METADATA_RESULTS/_delta_log/00000000000000000000.json
tests/luna/pathology/dsa/__init__.py
tests/luna/pathology/dsa/test_dsa_api_handler.py
tests/luna/pathology/dsa/test_utils.py
tests/luna/pathology/slideviewer/point_annotation/proxy_table/__init__.py
tests/luna/pathology/slideviewer/point_annotation/proxy_table/test_generate.py
tests/luna/pathology/slideviewer/point_annotation/refined_table/__init__.py
tests/luna/pathology/slideviewer/point_annotation/refined_table/test_generate.py
tests/luna/pathology/slideviewer/point_annotation/testdata/point_geojson_config.yaml
tests/luna/pathology/slideviewer/point_annotation/testdata/point_js_config.yaml
tests/luna/pathology/slideviewer/point_annotation/testdata/test-project/tables/POINT_RAW_JSON_dsn/part-00000-4706cb19-2c51-4d62-8d62-95807ce23a88-c000.snappy.parquet
tests/luna/pathology/spatial/test_stats.py
tests/luna/pathology/spatial/test_transforms.py
tests/luna/pathology/testdata/data/tables/patient/part-00000-5025e773-99df-4136-a1f4-342047751fa6-c000.snappy.parquet
tests/luna/pathology/testdata/data/tables/patient/_delta_log/00000000000000000000.json
tests/luna/pathology/testdata/data/test-project/configs/REGIONAL_CONCAT_GEOJSON_ds/app_config.yaml
tests/luna/pathology/testdata/data/test-project/configs/REGIONAL_CONCAT_GEOJSON_ds/data_config.yaml
tests/luna/pathology/testdata/data/test-project/configs/REGIONAL_GEOJSON_dsn/app_config.yaml
tests/luna/pathology/testdata/data/test-project/configs/REGIONAL_GEOJSON_dsn/data_config.yaml
tests/luna/pathology/testdata/data/test-project/configs/WSI_dsn/app_config.yaml
tests/luna/pathology/testdata/data/test-project/configs/WSI_dsn/data_config.yaml
tests/luna/pathology/testdata/data/test-project/pathology_annotations/regional_bmps/2021_HobS21_8_123/123_jill_SVBMP-123sdf_annot.bmp
tests/luna/pathology/testdata/data/test-project/pathology_annotations/regional_bmps/2021_HobS21_8_123/123_joe_SVBMP-123asd_annot.bmp
tests/luna/pathology/testdata/data/test-project/pathology_annotations/regional_geojsons/default_labels/2021_HobS21_8_123/123_jill_SVBMP-123sdf_annot_geojson.json
tests/luna/pathology/testdata/data/test-project/pathology_annotations/regional_geojsons/default_labels/2021_HobS21_8_123/123_joe_SVBMP-123asd_annot_geojson.json
tests/luna/pathology/testdata/data/test-project/pathology_annotations/regional_npys/2021_HobS21_8_123/123_jill_SVBMP-123sdf_annot.npy
tests/luna/pathology/testdata/data/test-project/pathology_annotations/regional_npys/2021_HobS21_8_123/123_joe_SVBMP-123asd_annot.npy
tests/luna/pathology/testdata/data/test-project/tables/REGIONAL_BITMASK_dsn/part-00000-699340cb-a72c-494c-818f-4cdfa17bab23-c000.snappy.parquet
tests/luna/pathology/testdata/data/test-project/tables/REGIONAL_BITMASK_dsn/part-00002-f36277fb-156d-4c44-a281-0b44ac58bd7d-c000.snappy.parquet
tests/luna/pathology/testdata/data/test-project/tables/REGIONAL_BITMASK_dsn/part-00005-8b16c280-b125-4caf-8a8b-8303a8b91548-c000.snappy.parquet
tests/luna/pathology/testdata/data/test-project/tables/REGIONAL_BITMASK_dsn/_delta_log/00000000000000000000.json
tests/luna/pathology/testdata/data/test-project/tables/REGIONAL_GEOJSON_ds/part-00000-4f3fc61c-c48e-4802-8d3c-228a93717724-c000.snappy.parquet
tests/luna/pathology/testdata/data/test-project/tables/REGIONAL_GEOJSON_ds/part-00008-a776da6a-7e2c-4b9e-a35d-205d2413e798-c000.snappy.parquet
tests/luna/pathology/testdata/data/test-project/tables/REGIONAL_GEOJSON_ds/part-00033-a7d97f34-f390-43f0-9bab-b7c400a5f01c-c000.snappy.parquet
tests/luna/pathology/testdata/data/test-project/tables/REGIONAL_GEOJSON_ds/_delta_log/00000000000000000000.json
tests/luna/pathology/testdata/test_dataset_address/dicom/RIA_12_345_001/20070401_CT/3_Lung_5mm/1.dcm
tests/luna/pathology/testdata/test_dataset_address/dicom/RIA_12_345_001/20070401_CT/3_Lung_5mm/2.dcm
tests/luna/pathology/testdata/test_dataset_address/dicom/RIA_12_345_001/20070401_CT/3_Lung_5mm/3.dcm
tests/luna/testdata/data/test-project/configs/WSI_dsn/app_config.yaml
tests/luna/testdata/data/test-project/configs/WSI_dsn/data_config.yaml