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This script could be used for conversion of a .tiff file to .zarr format with OME-NGFF multiscales metadata structure.
How to run
- open command line terminal
- install poetry tool for dependency management and packaging: https://pypi.org/project/poetry/
- switch to the tif_to_zarr directory:
cd PATH_TO_DIRECTORY/tif_to_zarr - install python dependencies:
poetry install - run script using cli:
poetry run python src/tif_to_zarr.py --src=PATH_TO_SOURCE_DIRECTORY/input_file.tif --dest=PATH_TO_DEST_DIRECTORY/output_file.zarr - to convert a tiff file to zarr with custom metadata values, you can run smthg similar to this:
poetry run python3 src/tif_to_zarr.py --src=path_to_source_tif --dest=path_to_output_zarr -a x z y -t 1.0 2.0 3.0 -s 4.0 5.0 6.0 -u nanometer nanometer nanometer - To get the list of options, you may run this:
poetry run python3 src/tif_to_zarr.py --help
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