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Hatch

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:

  1. 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.

  2. Only transfers max size from original source files and drops all other images including cover slide images

  3. 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