# Getting started

Use Pathology Explorer in Claude, via MCP (Model Context Protocol), to query TCGA H\&E slides. Browse cohorts, view thumbnails and tiles, run survival analyses, and export features.

### Connect Pathology Explorer to Claude

#### Prerequisites

* An Owkin account (create a free account at [k.owkin.com](https://k.owkin.com/auth/signup?next=%2Fchat)).
* A paid Claude plan (Pro, Max, Team, or Enterprise).
* Claude Custom Connectors enabled for your workspace.

The integration uses Claude’s **remote MCP custom connector** flow. Claude Free does not support this. See Anthropic’s guide: [Getting started with custom connectors using remote MCP](https://support.claude.com/en/articles/11175166-getting-started-with-custom-connectors-using-remote-mcp).

#### Claude.ai (web)

{% stepper %}
{% step %}

### Add the connector (workspace admin)

Go to **Admin settings** → **Connectors** → **Add custom connector**.

Enter:

* **Name:** `Owkin`
* **URL:** `https://mcp.k.owkin.com/mcp`

Leave **OAuth Client ID** and **OAuth Client Secret** empty.
{% endstep %}

{% step %}

### Connect and authenticate

Go to **Settings** → **Connectors**.

Click **Connect** next to **Owkin**.

Approve the access request. Then sign in to Owkin.

![](https://docs.owkin.com/~gitbook/image?url=https%3A%2F%2F1398098133-files.gitbook.io%2F%7E%2Ffiles%2Fv0%2Fb%2Fgitbook-x-prod.appspot.com%2Fo%2Fspaces%252FsQnMGEZUFMazkLv5a4BR%252Fuploads%252Fgit-blob-b6d1aea382214f2352ccdc3196675f8fab3f4187%252FOwkinMCPLogin.png%3Falt%3Dmedia\&width=768\&dpr=3\&quality=100\&sign=492f89d3\&sv=2)
{% endstep %}

{% step %}

### Verify the connection

Start a new chat and ask:

```
Can you list the available TCGA cohorts?
```

If it works, Claude returns a cohort list from Owkin.
{% endstep %}
{% endstepper %}

#### Claude Desktop

If you’re on a Team/Enterprise workspace, the connector added by an admin should appear on Desktop too.

1. Open **Settings** → **Connectors**.
2. Click **Connect** next to **Owkin**.
3. Sign in to Owkin when redirected.
4. Run the same verification prompt.

{% hint style="info" %}
If you don’t see **Connectors** (or **Owkin** is missing), your workspace may not allow custom connectors. Ask your Claude admin.
{% endhint %}

### Troubleshooting

{% hint style="warning" %}
**Sign-in page looks stuck**

The auth page can appear to hang. The connection may still succeed.

Go back to Claude and run the verification prompt.
{% endhint %}

{% hint style="warning" %}
**Error: “Invalid or expired transaction”**

This usually happens after clicking **Allow access** twice.

Retry in a different browser. This is a known Chrome issue with `claude://` redirects.
{% endhint %}

{% hint style="warning" %}
**Connected, but tools don’t show up**

* Confirm you connected the **Owkin** connector in **Settings → Connectors**.
* Re-check the URL: `https://mcp.k.owkin.com/mcp`.
* Restart Claude after changes.
  {% endhint %}

{% hint style="warning" %}
**Session expired**

Sessions currently last **15 minutes**.

Disconnect and reconnect the Owkin connector in **Settings → Connectors**.
{% endhint %}

If you still can’t connect, submit a support request using this [form](https://owkinkhelp.zendesk.com/hc/en-us/requests/new?ticket_form_id=41391636133649).

### What you can do with Pathology Explorer

Pathology Explorer is built for cohort exploration and hypothesis testing on TCGA histology.

It is powered by Owkin’s model (see paper: <https://arxiv.org/abs/2508.09926>). It supports slide-level features and tile visualizations.

#### Example prompts

**Find cohorts and cases**

```
List the TCGA cohorts you support. Then show me the cohorts with the most slides.
```

**Stratify patients by immune infiltration**

```
In TCGA_LUAD, find slides with low lymphocyte density. Summarize patient-level trends.
```

**Find “most enriched” slides and plot**

```
In TCGA_BRCA, find the slide most enriched in eosinophils and show the thumbnail.
```

**Run survival analysis**

```
In TCGA_BLCA, is plasmocyte density associated with overall survival? Use OS and stratify patients.
```

**Export features for reproducibility**

```
Export histomics data for cohort TCGA_LUAD as parquet.
```

### Data and outputs

#### Available data

You can query TCGA cohorts available in this integration. Use:

```
List the available TCGA cohorts.
```

For the current cohort coverage list, also see [Extended features description for Pathology Explorer](https://docs.owkin.com/core-features-and-usage/pathology-explorer-mcp-ai-powered-tissue-analysis/understanding-pathology-explorers-analysis-capabilities).

#### Cell types

The model detects **six cell types** on H\&E. Ask for the exact list:

```
List the available cell types.
```

#### Outputs you can retrieve

* Slide thumbnails.
* Tile mosaics with predictions.
* Slide-level histomics features.
* Parquet exports for downstream analysis.

### Tool reference (advanced)

<details>

<summary>Show the MCP tools exposed by the connector</summary>

* **Pathology Explorer description**: summary of model and capabilities.
* **List available cell types**: returns the supported cell types.
* **List TCGA cohorts**: returns supported TCGA cohorts.
* **Describe slide-level histomics features**: describes feature names and meanings.
* **Filter slides by histomics features**: returns slide IDs matching feature criteria.
* **Get histomics features for slides**: returns features for specific slide IDs.
* **Display slide thumbnail**: renders a slide thumbnail.
* **Perform survival analysis**: runs OS/PFS survival analysis on a cohort.
* **Download histomics data**: presigned URL for Parquet download.
* **Filter tiles by histomics**: selects tiles by feature criteria.
* **Display tiles with predictions**: renders a tile mosaic with predictions.

</details>