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 (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)
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.
By default, two additional readers (MiraxReader and PyramidTiffReader) are added to the beginning of Bio-Formats' list of reader classes.
Either or both of these readers can be excluded with the --extra-readers option:
# only include the reader for .mrxs, exclude the reader for Faas pyramids
bin/bioformats2raw /path/to/file.tiff /path/to/n5-pyramid --extra-readers com.glencoesoftware.bioformats2raw.MiraxReader
# don't add any additional readers, just use the ones provided by Bio-Formats
bin/bioformats2raw /path/to/file.mrxs /path/to/n5-pyramid --extra-readers