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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.
For basic usage see the documentation page "How do I...?".
There are many other great tools in this space. Below are some other tools for converting WSIs.
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/
Convert from Bio-Formats formats to zarr.
https://github.com/glencoesoftware/bioformats2raw
Convert from Philips' iSyntax format to a zarr.
https://github.com/glencoesoftware/isyntax2raw
Convert OpenSlide images to WSI DICOM.
https://github.com/sectra-medical/wsidicomizer
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
-s
argment for convert
to specify store for zarr.DICOMWSIReader
required user input at init.TIFFWriter
pyramid building.DICOMWSIReader
init warning and only warn from the main process.ZarrReaderWriter
to seperate ZarrWriter
and ZarrReader
.CoordinateTransformation
field default factor.get_tile
method to all Reader
classes.pyramid_downsamples
argument when None
.FAQs
Whole Slide Image (WSI) conversion for brightfield histology images
We found that wsic demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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