wsi_extraction --config path/to/config.yaml

wsi_extraction [-h]
    [--wsi_paths WSI_PATHS]
    [--wsi_filelist WSI_FILELIST]
    [--output_path OUTPUT_PATH]
    [--wsi_extension {svs}]
    [--config CONFIG]
    [--patch_size PATCH_SIZE]
    [--patch_overlap PATCH_OVERLAP]
    [--target_mpp TARGET_MPP]
    [--target_mag TARGET_MAG]
    [--downsample DOWNSAMPLE]
    [--level LEVEL]
    [--context_scales [CONTEXT_SCALES ...]]
    [--check_resolution CHECK_RESOLUTION]
    [--processes PROCESSES]
    [--overwrite]
    [--annotation_paths ANNOTATION_PATHS]
    [--annotation_extension {json,xml}]
    [--incomplete_annotations]
    [--label_map_file LABEL_MAP_FILE]
    [--save_only_annotated_patches]
    [--save_context_without_mask]
    [--exclude_classes EXCLUDE_CLASSES]
    [--store_masks]
    [--overlapping_labels]
    [--normalize_stains]
    [--normalization_vector_json NORMALIZATION_VECTOR_JSON]
    [--min_intersection_ratio MIN_INTERSECTION_RATIO]
    [--tissue_annotation TISSUE_ANNOTATION]
    [--tissue_annotation_intersection_ratio TISSUE_ANNOTATION_INTERSECTION_RATIO]
    [--masked_otsu]
    [--otsu_annotation OTSU_ANNOTATION]
    [--filter_patches FILTER_PATCHES]
    [--apply_prefilter APPLY_PREFILTER]
    [--log_path LOG_PATH]
    [--log_level {critical,error,warning,info,debug}]
    [--hardware_selection {cucim,openslide}]
    [--wsi_magnification WSI_MAGNIFICATION]
    [--wsi_mpp WSI_MPP]

options:
  -h, --help            show this help message and exit
  --wsi_paths WSI_PATHS
                        Path to the folder where all WSI are stored or path to a
                        single WSI-file. (default: None)
  --wsi_filelist WSI_FILELIST
                        Path to a csv-filelist with WSI files (separator: `,`), if
                        provided just these files are used.Must include full paths
                        to WSIs, including suffixes.Can be used as an replacement
                        for the wsi_paths option.If both are provided, yields an
                        error. (default: None)
  --output_path OUTPUT_PATH
                        Path to the folder where the resulting dataset should be
                        stored. (default: None)
  --wsi_extension {svs,tiff,tif,bif,scn,ndpi,vms,vmu}
                        The extension types used for the WSI files, the options
                        are: ['svs', 'tiff', 'tif', 'bif', 'scn', 'ndpi', 'vms',
                        'vmu'] (default: None)
  --config CONFIG       Path to a config file. The config file can hold the same
                        parameters as the CLI. Parameters provided with the CLI are
                        always having precedence over the parameters in the config
                        file. (default: None)
  --patch_size PATCH_SIZE
                        The size of the patches in pixel that will be retrieved
                        from the WSI, e.g. 256 for 256px (default: None)
  --patch_overlap PATCH_OVERLAP
                        The percentage amount pixels that should overlap between
                        two different patches. Please Provide as integer between 0
                        and 100, indicating overlap in percentage. (default: None)
  --target_mpp TARGET_MPP
                        If this parameter is provided, the output level of the WSI
                        corresponds to the level that is at the target microns per
                        pixel of the WSI. Alternative to target_mag, downsaple and
                        level. Highest priority, overwrites all other setups for
                        magnifcation, downsample, or level. (default: None)
  --target_mag TARGET_MAG
                        If this parameter is provided, the output level of the WSI
                        corresponds to the level that is at the target
                        magnification of the WSI. Alternative to target_mpp,
                        downsaple and level. High priority, just target_mpp has a
                        higher priority, overwrites downsample and level if
                        provided. (default: None)
  --downsample DOWNSAMPLE
                        Each WSI level is downsampled by a factor of 2, downsample
                        expresses which kind of downsampling should be used with
                        respect to the highest possible resolution. Medium
                        priority, gets overwritten by target_mag and target_mpp if
                        provided, but overwrites level. (default: None)
  --level LEVEL         The tile level for sampling, alternative to downsample.
                        Lowest priority, gets overwritten by target_mag and
                        downsample if they are provided. (default: None)
  --context_scales [CONTEXT_SCALES ...]
                        Define context scales for context patches. Context patches
                        are centered around a central patch. The context-patch size
                        is equal to the patch-size, but downsampling is different
                        (default: None)
  --check_resolution CHECK_RESOLUTION
                        If a float value is supplies, the program checks whether
                        the resolution of all images corresponds to the given value
                        (default: None)
  --processes PROCESSES
                        The number of processes to use. (default: None)
  --overwrite           Overwrite the patches that have already been created in
                        case they already exist. Removes dataset. Handle with care!
                        (default: None)
  --annotation_paths ANNOTATION_PATHS
                        Path to the subfolder where the XML/JSON annotations are
                        stored or path to a file (default: None)
  --annotation_extension {json}
                        The extension types used for the annotation files, the
                        options are: ['json'] (default: None)
  --incomplete_annotations
                        Set to allow WSI without annotation file (default: None)
  --label_map_file LABEL_MAP_FILE
                        The path to a json file that contains the mapping between
                        the annotation labels and some integers; an example can be
                        found in examples (default: None)
  --save_only_annotated_patches
                        If true only patches containing annotations will be stored
                        (default: None)
  --save_context_without_mask
                        This is helpful for extracting patches, that are not within
                        a mask, but needed for the Valuing Vicinity Segmentation
                        Algorithms. This flag is specifically helpful if only fully
                        annotated patches should be extracted from a region of
                        interest (ROI) and their masks are stored, but also
                        sourrounding neighbourhood patches (without mask) are
                        needed. (default: None)
  --exclude_classes EXCLUDE_CLASSES
                        Can be used to exclude annotation classes (default: None)
  --store_masks         Set to store masks per patch. Defaults to false (default:
                        None)
  --overlapping_labels  Per default, labels (annotations) are mutually exclusive.
                        If labels overlap, they are overwritten according to the
                        label_map.json ordering (highest number = highest priority)
                        (default: None)
  --normalize_stains    Uses Macenko normalization on a portion of the whole slide
                        image (default: None)
  --normalization_vector_json NORMALIZATION_VECTOR_JSON
                        The path to a JSON file where the normalization vectors are
                        stored (default: None)
  --adjust_brightness   Normalize brightness in a batch by clipping to 90 percent.
                        Not recommended, but kept for legacy reasons (default:
                        None)
  --min_intersection_ratio MIN_INTERSECTION_RATIO
                        The minimum intersection between the tissue mask and the
                        patch. Must be between 0 and 1. 0 means that all patches
                        are extracted. (default: None)
  --tissue_annotation TISSUE_ANNOTATION
                        Can be used to name a polygon annotation to determine the
                        tissue area. If a tissue annotation is provided, no Otsu-
                        thresholding is performed (default: None)
  --tissue_annotation_intersection_ratio TISSUE_ANNOTATION_INTERSECTION_RATIO
                        Intersection ratio with tissue annotation. Helpful, if ROI
                        annotation is passed, which should not interfere with
                        background ratio. If not provided, the default
                        min_intersection_ratio with the background is used.
                        (default: None)
  --masked_otsu         Use annotation to mask the thumbnail before otsu-
                        thresholding is used (default: None)
  --otsu_annotation OTSU_ANNOTATION
                        Can be used to name a polygon annotation to determine the
                        area for masked otsu thresholding. Seperate multiple labels
                        with ' ' (whitespace) (default: None)
  --filter_patches      Post-extraction patch filtering to sort out artefacts,
                        marker and other non-tissue patches with a DL model. Time
                        consuming. Defaults to False. (default: None)
  --apply_prefilter     Pre-extraction mask filtering to remove marker from mask
                        before applying otsu. Defaults to False. (default: None)
  --log_path LOG_PATH   Path where log files should be stored. Otherwise, log files
                        are stored in the output folder (default: None)
  --log_level {critical,error,warning,info,debug}
                        Set the logging level. Options are ['critical', 'error',
                        'warning', 'info', 'debug'] (default: None)
  --hardware_selection {cucim,openslide}
                        Select hardware device (just if available, otherwise always
                        cucim). Defaults to cucim. (default: None)
  --wsi_magnification WSI_MAGNIFICATION
                        Manual WSI magnification, but just applies if metadata
                        cannot be derived from OpenSlide (e.g., for .tiff files).
                        (default: None)
  --wsi_mpp WSI_MPP     Manual WSI MPP, but just applies if metadata cannot be
                        derived from OpenSlide (e.g., for .tiff files). (default:
                        None)

WSI_Name
├── annotation_masks      # thumbnails of extracted annotation masks
│   ├── all_overlaid.png  # all with same dimension as the thumbnail
│   ├── tumor.png
│   └── ...  
├── context               # context patches, if extracted
│   ├── 2                 # subfolder for each scale
│   │   ├── WSI_Name_row1_col1_context_2.png
│   │   ├── WSI_Name_row2_col1_context_2.png
│   │   └── ...
│   └── 4
│   │   ├── WSI_Name_row1_col1_context_2.png
│   │   ├── WSI_Name_row2_col1_context_2.png
│   │   └── ...
├── masks                 # Mask (numpy) files for each patch -> optional folder for segmentation
│   ├── WSI_Name_row1_col1.npy
│   ├── WSI_Name_row2_col1.npy
│   └── ...
├── metadata              # Metadata files for each patch
│   ├── WSI_Name_row1_col1.yaml
│   ├── WSI_Name_row2_col1.yaml
│   └── ...
├── patches               # Patches as .png files
│   ├── WSI_Name_row1_col1.png
│   ├── WSI_Name_row2_col1.png
│   └── ...
├── thumbnails            # Different kind of thumbnails
│   ├── thumbnail_mpp_5.png
│   ├── thumbnail_downsample_32.png
│   └── ...
├── tissue_masks          # Tissue mask images for checking
│   ├── mask.png          # all with same dimension as the thumbnail
│   ├── mask_nogrid.png
│   └── tissue_grid.png
├── mask.png              # tissue mask with green grid  
├── metadata.yaml         # WSI metdata for patch extraction
├── patch_metadata.json   # Patch metadata of WSI merged in one file
└── thumbnail.png         # WSI thumbnail