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]

  Convert a WSI.

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 [blosc|deflate|jpeg xl|jpeg-ls|jpeg|jpeg2000|lzw|png|webp|zstd]
                                  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-TIFF and
                                  NGFF).
  --overwrite / --no-overwrite    Whether to overwrite the output file.
  -to, --timeout FLOAT            Timeout in seconds for reading a tile.
  -W, --writer [auto|jp2|svs|tiff|zarr]
                                  The writer to use. Overrides writer detected
                                  by output file extension.
  -s, --store [dir|ndir|zip|sqlite]
                                  The store to use (zarr/NGFF only). Defaults
                                  to ndir (nested directory).
  -h, --help                      Show this message and exit.

Getting Started

For basic usage see the documentation page "How do I...?".

Features

• Reading and writing several container formats.
• Support for a wide range of compression codecs.
• Custom tile size
• Lossless repackaging / transcoding (to zarr/NGFF or TIFF) from:
  • SVS (JPEG compressed)
  • OME-TIFF (single image, JPEG and JPEG2000 (J2K) compressed)
  • Generic Tiled TIFF (JPEG, JPEG2000, and WebP compressed)
  • DICOM WSI (JPEG and JPEG2000 (J2K) compressed)

Read Container Formats

• 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)
  • Tiled with various codecs: e.g. JPEG XL, JPEG 2000, WebP, and zstd.
  • RGB/brightfield OME-TIFF.
• JP2 (via glymur and OpenJPEG)
  • Including Omnyx JP2 files.
• Zarr
  • Single array.
  • Group of (multiresolution) arrays.
  • NGFF v0.4.
• DICOM WSI (via wsidicom)
  • DICOM VL Whole Slide Image IODs.

Write Container Formats

• TIFF
  • Generic Tiled / Pyramid TIFF
  • OME-TIFF
  • SVS
• JP2
• Zarr (NGFF v0.4)
• DICOM (.dcm)

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.