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Bio-Formats whole slide imaging to raw format converter
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chris-allan Merge pull request #13 from perlman/compression_opts
Allow choice of alternate compression (gzip, etc).
Latest commit f0e6355 Jan 23, 2020
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config/checkstyle Add checkstyle configuration and update *.java to comply Nov 12, 2019
gradle/wrapper Initial progress on mrxs2ometiff Oct 19, 2019
src/main Move compression selection to a class. Jan 17, 2020
LICENSE.txt Unify license headers and switch to GPL 2+ Nov 12, 2019 Update documentation Nov 26, 2019
appveyor.yml Add minimal AppVeyor configuration Nov 11, 2019
build.gradle Change main class name to reflect new package Nov 25, 2019
gradlew Initial progress on mrxs2ometiff Oct 19, 2019
gradlew.bat Initial progress on mrxs2ometiff Oct 19, 2019

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.


libblosc ( 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 (


Build with Gradle:

gradle clean build

Unpack the distribution:

cd build/distributions
unzip bioformats2raw-$
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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