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raw2ometiff converter

Java application to convert a directory of tiles to an OME-TIFF pyramid. This is the second half of iSyntax/.mrxs => OME-TIFF conversion.

Requirements

Java 8 or later is required.

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
  • Ubuntu 18.04+: apt-get install libblosc1

Installation

  1. Download and unpack a release artifact:

    https://github.com/glencoesoftware/raw2ometiff/releases

Development Installation

  1. Clone the repository:

    git clone git@github.com:glencoesoftware/raw2ometiff.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 (Bio-Formats 6.x):

raw2ometiff tile_directory pyramid.ome.tiff

or generate a 5.9.x-compatible pyramid:

raw2ometiff tile_directory pyramid.tiff --legacy

The input tile directory must contain a full pyramid in a Zarr container.

By default, LZW compression will be used in the OME-TIFF file. The compression can be changed using the --compression option. Tile compression is performed in parallel. The number of workers can be changed using the --max_workers option.

axes and transformations metadata in the input Zarr will be ignored. This metadata is assumed to be consistent with the corresponding PhysicalSize*, TimeIncrement, and DimensionOrder values in the input METADATA.ome.xml.

Areas to improve

  • Compatibility with both iSyntax and .mrxs
    • map JSON metadata to OME-XML (magnification etc.)
    • fix tile sizes used when downsampling (TIFF input only)

License

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

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Raw format to OME-TIFF converter

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