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bioformats2raw converter

Java application to convert image file formats, including .mrxs, to an intermediate 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.

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 jzarr readme (https://github.com/bcdev/jzarr/blob/master/README.md)

  • Mac OSX: brew install c-blosc then set the JAVE_OPTS enviroment variable (example: echo export JAVA_OPTS='-Djna.library.path=/usr/local/Cellar/c-blosc/*/lib' >> ~/.zshrc ). (Note: make sure the path is to the folder containing libblosc.dylib and not path to libblosc.dylib itself).

  • Windows: Install latest version of blosc (https://sites.imagej.net/N5/lib/win64/). Rename file to blosc.dll and set the JAVE_OPTS enviroment variable (example: set JAVA_OPTS="-Djna.library.path=C:\path\to\blosc\folder"). (Note: make sure the path is to the folder containing blosc.dll and not path to blosc.dll itself).

  • Ubuntu 18.04+: apt-get install libblosc1 then set the JAVE_OPTS enviroment variable.

Installation

  1. Download and unpack a release artifact:

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

Development Installation

  1. Clone the repository:

    git clone git@github.com:glencoesoftware/bioformats2raw.git

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

    ./gradlew tasks

Eclipse Configuration

  1. Run the Gradle Eclipse task:

    ./gradlew eclipse

Usage

Run the conversion:

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

If the input file has multiple series, a subset of the series can be converted by specifying a comma-separated list of indexes:

bioformats2raw /path/to/file.scn /path/to/zarr-pyramid --series 0,2,3,4

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/zarr-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/zarr-pyramid --extra-readers

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

bioformats2raw /path/to/file.mrxs /path/to/zarr-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/zarr-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.

Usage Changes

Versions 0.2.6 and prior supported both N5 and Zarr output using the --file_type option. This option is not present in 0.3.0 and later, as only Zarr output is supported.

Versions 0.2.6 and prior used the input file's dimension order to determine the output dimension order, unless --dimension-order was specified. Version 0.3.0 uses the TCZYX order by default, for compatibility with https://ngff.openmicroscopy.org/0.2/#image-layout. The --dimension-order option can still be used to set a specific output dimension order, e.g.:

bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid --dimension-order XYCZT

or can be set to use the input file's ordering, preserving the behavior of 0.2.6:

bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid --dimension-order original

If a specific dimension order is passed to --dimension-order, it must be a valid dimension order as defined in the OME 2016-06 schema. The specified dimension order is then reversed when creating Zarr arrays, e.g. XYCZT would become TZCYX in Zarr.

Prior to version 0.3.0, N5/Zarr output was placed in a subdirectory (data.[n5|zarr]) with a METADATA.ome.xml file at the same level. As of 0.3.0 the desired output directory is now a Zarr group and the METADATA.ome.xml file is placed in a OME directory within. These changes reflect layout version 3.

Performance

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.

The worker count defaults to the number of detected CPUs. This may or may not be appropriate for the chosen input data. If reading a single tile from the input data requires a lot of memory, decreasing the worker count will be necessary to prevent memory exhaustion. JPEG, PNG, and certain TIFFs are especially susceptible to this problem.

The worker count should be set to 1 if the input data requires a Bio-Formats reader that is not thread-safe. This is not a common case, but is a known issue with Imaris HDF data in particular.

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

License

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