This tool converts the largest image in a VSI, SVS, or TIF image into a new TIFF image with a freshly created image pyramid with each scaling 1/2 dimensions each scale.
Features:
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Hatch transfers raw jpeg encodings from original image to new image to prevent any re-encoding image loss due to re-compression. OME Bioformats always decodes and then re-encodes when using their tools like bfconvert.
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Only transfers max size from original source files and drops all other images including cover slide images
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image pyramid is re-created from original image
Build with:
Jar version
mvn -Pjar clean package
Native-image version (requires fully configured Graalvm native-image environment)
mvn -Pnative clean package
Usage:
hatch -src <src> -dest <dest>
or see
hatch -help
Credits and Acknowledgements: Many of the core files are modified files from the OME Bioformats Projects (https://github.com/ome/bioformats) such as (but not limited to): CellSensReader TiffCompression TiffParser