Java application to convert image file formats, including .mrxs, to an intermediate N5/Zarr 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)

• Mac OSX: brew install c-blosc
• Ubuntu 18.04+: apt-get install libblosc1

1. Download and unpack a release artifact:

   https://github.com/glencoesoftware/bioformats2raw/releases

1. Clone the repository:

   git clone [email protected]:glencoesoftware/bioformats2raw.git

2. Run the Gradle build as required, a list of available tasks can be found by running:

   ./gradlew tasks

1. Run the Gradle Eclipse task:

   ./gradlew eclipse

Run the conversion:

bioformats2raw /path/to/file.mrxs /path/to/n5-pyramid --resolutions 6
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 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
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
bioformats2raw /path/to/file.mrxs /path/to/n5-pyramid --extra-readers

Reader-specific options can be specified using --options:

bioformats2raw /path/to/file.mrxs /path/to/n5-pyramid --options mirax.use_metadata_dimensions=false

Be aware when experimenting with different values for --options that the corresponding memo (cache) file may need to be removed in order for new options to take effect. This file will be e.g. /path/to/.file.mrxs.bfmemo.

The output in /path/to/n5-pyramid can be passed to raw2ometiff to produce an OME-TIFF that can be opened in ImageJ, imported into OMERO, etc. See https://github.com/glencoesoftware/raw2ometiff for more information.

This package is highly sensitive to underlying hardware as well as the following configuration options:

• --max_workers
• --tile_width
• --tile_height

On systems with significant I/O bandwidth, particularly SATA or NVMe based storage, you may find sharply diminishing returns with high worker counts. There are significant performance gains to be had utilizing larger tile sizes but be mindful of the consequences on the downstream workflow.

In general, expect to need to tune the above settings and measure relative performance.

The converter is distributed under the terms of the GPL license. Please see LICENSE.txt for further details.