--- a +++ b/resources/config.json @@ -0,0 +1,28 @@ +{"use_tissue_detection": true, + "tissue_coverage": 0.7, + "keep_annotated_tiles_despite_too_little_tissue_coverage": false, + "processing_level": 5, + "blocked_threads": 4, + "patches_per_tile": 8, + "overlap": 0.25, + "annotation_overlap": 0.25, + "patch_size": 256, + "calibration": {"use_non_pixel_lengths": true, "patch_size_microns": 64, "resize": true}, + "slides_file": "/home/katja/Data/svs-WSIs/slides_file.txt", + "slides_dir": "/home/katja/Data/svs-WSIs/", + "annotation_dir": "/home/katja/Data/svs-WSIs/test_project", + "annotation_file_format": "geojson", + "output_path": "/home/katja/Data/svs-WSIs/tiles/", + "skip_unlabeled_slides": false, + "save_annotated_only": false, + "output_format": "jpeg", + "metadata_format": "json", + "show_mode": false, + "label_dict": { + "non_tumor": {"type": "==", "threshold": 1.0, "annotated": false}, + "Tumor": {"type": ">=", "threshold": 0.5, "annotated": true}, + "Necrosis": {"type": ">=", "threshold": 0.5, "annotated": true}, + "Stroma": {"type": ">=", "threshold": 0.5, "annotated": true} + }, + "overlapping_annotations_verbose": true +} \ No newline at end of file