ZarrSeg

Command line tool to segment local and remote OME-Zarr data

Installation:

pip install git+https://github.com/Euro-BioImaging/ZarrSeg.git

Example command line to threshold local OME-Zarr:

zseg threshold -m otsu -c 1 -ch 0 -n otsu-c1-ch0 --colormap viridis /path/to/example.zarr

The command line arguments:

-m: the threshold method, which here is the Otsu method.
-c: the coefficient, that is multiplied with the threshold found by the method specified with -m.
-ch: the channel that is to be thresholded. Needed if the input OME-Zarr has multiple channels.
-n: the name of the output. This will be the folder name created for this segmentation under the labels path
--colormap: colormap that is used to display the label image with napari-ome-zarr. Any of the matplotlib colormaps can be specified.