Java application to convert a directory of tiles to an OME-TIFF pyramid. This is the second half of iSyntax/.mrxs => OME-TIFF conversion.
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
Download and unpack a release artifact:
Clone the repository:
git clone email@example.com:glencoesoftware/raw2ometiff.git
Run the Gradle build as required, a list of available tasks can be found by running:
Run the Gradle Eclipse task:
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
Tile compression is performed in parallel. The number of workers can be changed using the
transformations metadata in the input Zarr will be ignored. This metadata is assumed to be consistent
with the corresponding
DimensionOrder values in the input
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)
The converter is distributed under the terms of the GPL license.
LICENSE.txt for further details.