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, 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
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