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Bio-Formats whole slide imaging to raw format converter
Java
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chris-allan Merge pull request #13 from perlman/compression_opts
Allow choice of alternate compression (gzip, etc).
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README.md

bioformats2raw converter

Java application to convert whole slide imaging file formats, including .mrxs, to an intermediate N5 structure. The raw2ometiff application can then be used to produce a Bio-Formats 5.9.x ("Faas") or Bio-Formats 6.x (true OME-TIFF) pyramid.

Requirements

libblosc (https://github.com/Blosc/c-blosc) version 1.9.0 or later must be installed separately. The native libraries are not packaged with any relevant jars. See also note in n5-zarr readme (https://github.com/saalfeldlab/n5-zarr/blob/0.0.2-beta/README.md)

Usage

Build with Gradle:

gradle clean build

Unpack the distribution:

cd build/distributions
unzip bioformats2raw-$VERSION.zip
cd bioformats2raw-$VERSION

Run the conversion:

bin/bioformats2raw /path/to/file.mrxs /path/to/n5-pyramid --resolutions 6
bin/bioformats2raw /path/to/file.svs /path/to/n5-pyramid --resolutions 6

Maximum tile dimensions are can be configured with the --tile_width and --tile_height options. Defaults can be viewed with bin/bioformats2raw --help. --resolutions is optional; if omitted, the number of resolutions is set so that the smallest resolution is no greater than 256x256.

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