omero-integration
Category: lab-automation · License: MIT · Version: 1.4 · Includes scripts
Tags: microscopy, image data management, OMERO, bioimaging
When to use it
Securely inspect and automate microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and documented OMERO.web APIs. Use for scoped OMERO inventory, metadata export, import/export planning, or reviewed write workflows.Example requests
Ask your agent in plain language, for example:- “List the datasets in my OMERO project 4512 and tell me how many images each has.”
- “I need the key-value map annotations and ROI shapes for images 88101, 88102 and 88107 on omero.ourlab.edu (group ‘Kessler_Lab’) exported to JSON for a figure legend. My script keeps failing with ‘Ice.ConnectionRefusedException’ when I use port 4064. The server is 5.6.x and I’m on Python 3.13.”
- “Our microscopy core stores a few hundred confocal stacks on a shared imaging server, and I want to move one finished screening plate’s worth of images to a collaborator as OME-TIFFs without pulling in the rest of the group’s unpublished data. How should I go about it?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole lab-automation category with /plugin install lab-automation@research-agent-skills.