Python library and OMERO CLI plugin to manage OME-Zarr labels in OMERO.
OME-Zarr groups containing label images can be linked to individual OMERO images as ROIs containing a single Mask shape as defined in the omero-zarr-pixel-buffer extension.
- Python 3.10 or later
omero-label is distributed via PyPI and can be installed using the standard
Python packaging managers like pip:
pip install omero-label
To register an OME-Zarr label, run the omero label register using the absolute
path to the label group and the ID of the image to link the label to:
omero label register /path/to/image.zarr/0/labels/my_label <image_id>
A successful registration will return the ID of the new object as Roi:<roi_id>.
To register an OME-Zarr label hosted on object storage, pass the S3 URL as
defined in omero-zarr-pixel-buffer
to the omero label register command:
omero label register s3://<endpoint>/<bucket>/path/to/image.zarr/0/labels/my_label <image_id>
The path of the S3 URL must be percent-encoded as defined in RFC 3986. S3 paths containing literal percent-encoded octets are not supported.
The properties of a label image can be retrieved by calling the omero label get command
using the ID of the ROI:
omero label get <roi_id>
The command will return the properties as a list of key/value pairs:
x=0.0
y=0.0
width=1584.0
height=788.0
fillColor=-65436
uri=/data/image.zarr/0/labels/cells
Properties can also be retrieved individually by specifying their name as an argument:
omero label get <roi_id> x
omero label get <roi_id> width
omero label get <roi_id> fillColor
To update the location of an OME-Zarr label, run omero label update:
omero label update <roi_id> /new/path/to/image.zarr/0/labels/my_label
Clone the repository:
git clone https://github.com/glencoesoftware/omero-label
Build the project using the build module:
pip intall build
python -m build
omero-label is licensed under the terms of the GNU General Public License (GPL) v2.