wsic

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

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)

Notes & FAQs

Python on Windows handles multiprocessing
differenly
to POSIX/UNIX-like systems. I suggest using the Windows Subsystem for
Linux on Windows
to ensure that wsic functions correctly and efficiently.

Other Tools

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

1. bfconvert
   Part of the Bio-Formats command line tools. Uses bioformats to convert
   from many formats to OME-TIFF.
2. biofromats2raw
   Convert from Bio-Formats formats to zarr.
3. isyntax2raw Convert from Philips' iSyntax format to a zarr using Philips' SDK.
4. wsidicomiser Convert OpenSlide images to WSI DICOM.

Credits

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