WSI-to-PNG Converter

This command line tool lets you converts either a single or a folder or whole slide images (mrxs, ndpi) to a PNG.

It takes the following command line arguments:

--file-path: Path to the mrxs single file or folder of files.

--output-path: Path to the output folder. The output format is the same name as the mrxs file, with an appendix if multiple patches are extracted.

--level: Optional. Level of the mrxs file that should be used for the conversion (default is 0).

--thumbnail: Optional. Default is False. If set, the thumbnail images are extracted (overrules --level).

--staining: Optional. Staining identifier, that would be specified right before .mrxs (e.g. CD8) (optional, default is '')

--override: Optional. Default is False. If set to True, overrides patches with the same file name in the output folder.

Run as python wsi_to_png.py [command line arguments].

ASAP-to-PNG Converter

This command line tool lets you extract patches a single or a folder or whole slide images (mrxs, ndpi) to a PNG based on rectangle annotations in a xml file (exported from ASAP).

It takes the following command line arguments:

--file-path: Path to the mrxs single file or folder of files.

--output-path: Path to the output folder. The output format is the same name as the mrxs file, with an appendix if multiple patches are extracted.

--xmls-path: Path to the coordinate xml files (created with rectangle tool in ASAP) single file or folder of files. If not provided, the full image is converted into a png.

--coord-annotation-tag: Name of the annotation group in the xml file (default is 'hotspot').

--matched_files_excel: Optional. If provided, then this file will be used to match the xmls to the mrxs file names (needs to contain a column called "WSI-names" and "XML-names"

--search-pattern: Search pattern, that is added after the folder (optional, default is '*' = all files)

--level: Level of the mrxs file that should be used for the conversion (default is 0).

--override: Default is False. If set to True, overrides patches with the same file name in the output folder.

Run as python asap_to_png.py [command line arguments].

TMA-to-PNG-converter

This is a more specific implementation, which cuts out TMA spots and saves them as a PNG file based on coordinates and the radius in a csv file.

--file-path: Path to the mrxs file.

--output-path: Path to the output folder. The output format is the same name as the mrxs file, with an appendix if multiple patches are extracted.

--coord_csv-path: Path to the csv file. Expects this set of headers: "Centroid X (pixels)", "Centroid Y (pixels)", "Radius (pixels)" (in pixel values)

--level: Level of the mrxs file that should be used for the conversion (default is 0). Needs to match the level of the pixel coordinates.

--staining: Staining identifier, that would be specified right before .mrxs (e.g. CD8) (optional, default is '')

--override: Default is False. If set to True, overrides patches with the same file name in the output folder.

--adjust_coord: Default is True. Adjusts coordinates extracted with QuPath for the missing white border in MRXS files. (Not necessary for ASAP extracted coordinates, or other file types).

Run as python tma_to_png.py [command line arguments].

Installation

You can set up the conda environment by running conda env create -f environment.yml in this directory. The tool the OpenSlide Python API is used to to handle the whole slide image files.

General Information

The level specified downsamples the images as follows: [1, 2, 4, 8, 16, 32, 64, 128, 256], where the level is the index in the list. E.g. level = 0 is the original image size, level = 3 downsamples the image by a factor of 4.