Working with Claude

You can run OMERO-Screen by talking to Claude instead of typing commands. Claude runs the tools for you, explains what it is doing, and asks before it changes anything in OMERO. This page sets that up. It takes about ten minutes.

What you need

  • The Claude desktop app (claude.ai/download), signed in.
  • OMERO-Screen installed with the one-line installer (Install & configure). The installer ends with omero-screen setup, which saves your OMERO login.
  • For OMERO from outside the university, the VPN.

1. Install the OMERO-Screen plugin

The plugin teaches Claude how OMERO-Screen works.

  1. Open the Claude desktop app.

  2. Go to Customize → Plugins.

  3. Choose Add marketplace and paste:

    HocheggerLab/omero-screen

  4. Find omero-screen in the list and click Install.

The plugin updates itself when we publish improvements.

Note

If your lab uses a Claude Team plan, the administrator can install the plugin for everyone (Organization settings → Plugins & skills → Sync from GitHub, repository HocheggerLab/omero-screen). You then skip this step.

2. Start a session that can use your computer

OMERO-Screen runs on your computer: napari opens windows on your screen, and OMERO is reached over your network. Claude therefore has to work on your computer, not only in the cloud.

  • Start a session in the desktop app with access to a folder on your computer, for example a Claude folder in your Documents. This is where Claude saves figures and tables.

  • Test it. Ask:

    Check my OMERO-Screen installation.

    Claude should run omero-screen doctor and report a list of checks. If it says it cannot run commands on your computer, use the Code tab of the desktop app instead; it looks like a chat too, runs on your computer, and uses the same plugin.

3. Things to ask

Start with something small, and say what you want in your own words. Claude will ask when it needs a plate number or a channel name.

Check and look

Check my OMERO-Screen installation.

Which plates do I have in OMERO? Show me plate 1234: wells, channels and cell lines.

Open plate 1234, well B3 in napari.

Train a classifier

I want to train a classifier that recognises micronuclei. Open plate 1234 in napari and help me collect example cells with and without micronuclei.

Train a classifier on the cells I collected and show me how well it does.

Publish the best model to OMERO and run it on plates 1234 and 1235.

Analyse and plot

Import plate 1234 into CellView.

Load plate 1234 from CellView and plot the γH2AX intensity per siRNA, as a PDF.

Make a cell-cycle plot for plates 1234 and 1235, controls first.

Good to know

  • Claude asks before changing OMERO: running the pipeline on a plate, publishing a classifier, deleting anything. Reading and plotting it does without asking.
  • Your password is never in the chat. If Claude says your login is missing, run omero-screen setup in Terminal yourself; it asks for the password there and keeps it in your keychain.
  • When something fails, ask Claude to run the check again. A failed connection is almost always the VPN.
  • Segmentation on a Mac uses the standard Cellpose 3 models, which work for most cells. For better masks, see Make a model for your cells.