# 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](installation.md)). 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: 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](models.md).