Script for converting images and segmentation masks to OME-Zarr. Images and masks can be converted to different OME-Zarr files or packed together in a single OME-Zarr file.
Install dependencies with:
pip install -r requirements
Convert an image or segmentation mask to OME-Zarr:
python convert_images_and_masks_to_omezarr.py /path/to/file
Convert an image and segmentation mask to OME-Zarr and pack them together in a single file:
python convert_images_and_masks_to_omezarr.py /path/to/image /path/to/mask
By default, the new Zarr file is created in the input image path, but an output file path can be specified using the --output_dirpath option:
python convert_images_and_masks_to_omezarr.py /path/to/image /path/to/mask --output_dirpath /path/to/output/directory