Java application to convert a directory of tiles to an OME-TIFF pyramid. This is the second half of iSyntax/.mrxs => OME-TIFF conversion.
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
-
Download and unpack a release artifact:
-
Clone the repository:
git clone git@github.com:glencoesoftware/raw2ometiff.git
-
Run the Gradle build as required, a list of available tasks can be found by running:
./gradlew tasks
-
Run the Gradle Eclipse task:
./gradlew eclipse
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 or N5 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.
- 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.
Please see LICENSE.txt for further details.