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).

• 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.

Claude.ai (web)

1

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.

2

Connect and authenticate

Go to Settings → Connectors.

Click Connect next to Owkin.

Approve the access request. Then sign in to Owkin.

3

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.

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.

If you don’t see Connectors (or Owkin is missing), your workspace may not allow custom connectors. Ask your Claude admin.

Troubleshooting

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.

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.

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.

Session expired

Sessions currently last 15 minutes.

Disconnect and reconnect the Owkin connector in Settings → Connectors.

If you still can’t connect, submit a support request using this form.

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.

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)

Show the MCP tools exposed by the connector

• 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.