> For the complete documentation index, see [llms.txt](https://docs.owkin.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.owkin.com/connect-and-integrate/pathology-explorer-mcp-ai-powered-tissue-analysis/getting-started.md). # 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: ). 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](/connect-and-integrate/pathology-explorer-mcp-ai-powered-tissue-analysis/understanding-pathology-explorers-analysis-capabilities.md). #### 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.
--- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://docs.owkin.com/connect-and-integrate/pathology-explorer-mcp-ai-powered-tissue-analysis/getting-started.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.