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Raw format to OME-TIFF converter
Java
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chris-allan Merge pull request #9 from melissalinkert/fix-legacy
Fix IFD writing when the "--legacy" option is used
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README.md

Build status

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

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)

Usage

Build with Gradle:

gradle clean build

Unpack the distribution:

cd build/distributions
unzip raw2ometiff-$VERSION.zip
cd raw2ometiff-$VERSION

Run the conversion (Bio-Formats 6.x):

bin/raw2ometiff tile_directory pyramid.ome.tiff

or generate a 5.9.x-compatible pyramid:

bin/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.

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)
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