tasks.harmony_to_ome_zarr

tasks.harmony_to_ome_zarr

Functions

Name Description
harmony_to_ome_zarr Convert TIFFs which were exported from Harmony (Operetta/Opera, Perkin-Elmer) to OME-ZARR

harmony_to_ome_zarr

tasks.harmony_to_ome_zarr.harmony_to_ome_zarr(zarr_urls, zarr_dir, img_paths, omero_channels, overwrite=False, coarsening_xy=2, compute=True)

Convert TIFFs which were exported from Harmony (Operetta/Opera, Perkin-Elmer) to OME-ZARR

Parameters

Name Type Description Default
zarr_urls list[str] List of zarr urls to be processed (not used by converter task) required
zarr_dir str Path to the new OME-ZARR output directory where the zarr plates should be saved. The zarr plates are extracted from the image paths required
img_paths list[str] Paths to the input directories with the image files required
omero_channels list[OmeroNgffChannel] List of Omero channels required
overwrite bool Whether to overwrite any existing OME-ZARR directory False
coarsening_xy int Coarsening factor in XY to use for downsampling when building the pyramids 2
compute bool Wether to compute a numpy array from the dask array while saving the image to the zarr fileset (compute = TRUE is faster given that images fit into memory) True