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)
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.