wsic 0.3.0

Whole Slide Image (WSI) conversion for brightfield histology images

wsic

Whole Slide Image (WSI) conversion for brightfield histology images.

Note: This is in early development and there will likely be frequent and breaking changes.

Provides a command line interface (CLI) for easy convertion between formats:

Usage: wsic convert [OPTIONS]

Options:
  -i, --in-path PATH              Path to WSI to read from.
  -o, --out-path PATH             The path to output to.
  -t, --tile-size <INTEGER INTEGER>...
                                  The size of the tiles to write.
  -rt, --read-tile-size <INTEGER INTEGER>...
                                  The size of the tiles to read.
  -w, --workers INTEGER           The number of workers to use.
  -c, --compression [deflate|webp|jpeg|jpeg2000]
                                  The compression to use.
  -cl, --compression-level INTEGER
                                  The compression level to use.
  -d, --downsample INTEGER        The downsample factor to use.
  -mpp, --microns-per-pixel <FLOAT FLOAT>...
                                  The microns per pixel to use.
  -ome, --ome / --no-ome          Save with OME-TIFF metadata (OME-XML).
  --overwrite / --no-overwrite    Whether to overwrite the output file.
  -h, --help                      Show this message and exit.

Features

• Read image data from:

  • OpenSlide Formats:

    • Aperio SVS (.svs)

    • Hamamatsu (.vms, .vmu, .ndpi)

    • Leica (.scn)

    • Mirax MRXS (.mrxs)

    • Sakura (.svslide)

    • Trestle (.tif)

    • Ventana (.bif, .tif)

    • Generic tiled TIFF (.tif; DEFLATE, JPEG, and Webp compressed)

  • Other Tiled TIFFs (tifffile supported formats)

  • OME-TIFF

  • JP2 (via glymur and OpenJPEG)

  • Zarr (single array or pyramid group of arrays)

  • DICOM WSI (via wsidicom)

• Write image data to:

  • Tiled / Pyramid Generic TIFF

  • OME-TIFF

  • JP2

  • Pyramid Zarr

• Custom tile size

• Compression codecs

• Lossless binary repackaging / transcoding mode (experimental) to zarr from:

  • SVS (JPEG / J2K compressed)

  • OME-TIFF (single image and JPEG / J2K compressed)

  • DICOM WSI (JPEG / J2K compressed)

Dependencies

• numpy

• zarr

• click (CLI)

Optional Dependencies

• OpenSlide and openslide-python (reading OpenSlide Formats)

• tifffile (reading tiled TIFFs)

• wsidicom (reading DICOM WSI)

• glymur and OpenJPEG (reading JP2)

• tqdm (progress bars)

• scipy (faster pyramid downsampling)

• opencv-python (even faster pyramid downsampling)

• imagecodecs (additional codecs and transcoding)

To-Dos

For a list of To-Dos see the project board.

Other Tools

There are many other great tools in this space. Below are some other tools for converting WSIs.

bfconvert

Part of the Bio-Formats command line tools. Uses bioformats to convert from many formats to OME-TIFF.

https://www.openmicroscopy.org/bio-formats/downloads/

biofromats2raw

Convert from Bio-Formats formats to zarr.

https://github.com/glencoesoftware/bioformats2raw

isyntax2raw

Convert from Philips’ iSyntax format to a zarr.

https://github.com/glencoesoftware/isyntax2raw

wsidicomiser

Convert OpenSlide images to WSI DICOM.

https://github.com/sectra-medical/wsidicomizer

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.1.0 (2022-02-22)

• First release on PyPI.

0.2.0 (2022-03-22)

• Add Support To Read DICOM WSI and transform to zarr.