omero-label

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.

Requirements

• Python 3.10 or later

Installation

omero-label is distributed via PyPI and can be installed using the standard Python packaging managers like pip:

pip install omero-label

Usage

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

Development

Clone the repository:

git clone https://github.com/glencoesoftware/omero-label

Build the project using the build module:

pip intall build
python -m build

License

omero-label is licensed under the terms of the GNU General Public License (GPL) v2.