Owkin

Query TCGA histopathology slides — cell-type quantification, tumour-microenvironment features, cohort survival.

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What the Owkin connector does

The Owkin MCP server connects Pathology Explorer — Owkin's AI model for reading H&E histology slides — to Claude, ChatGPT and any MCP-compatible agent. It turns public TCGA cancer slides into queryable numbers: cell-type counts, spatial tumor-microenvironment features and cohort survival analysis. Every listed tool reads, renders or exports. Sign-in is OAuth through Owkin.

Verified connector

Listed by Anthropic as a partner connector in its Connectors Directory.

Connection checked by Agentman on .

Anthropic states this reflects the level of review a connector received, not a security audit.

Owkin tools (9)

  • list_cell_types
  • list_cohorts
  • features_description
  • filter_slides
  • get_histomics
  • display_slide_thumbnail
  • survival_analysis
  • histoplus_help
  • download_histomics

Tool names from Anthropic's directory listing. This server requires sign-in, so we could not read tool descriptions or parameter schemas.

Limits

  • The listed tool count is stale by two releases. Anthropic lists 9; Owkin's changelog states 13 as of 2026-01-15. Owkin's own tool reference describes 11. Two tools are unaccounted for in every enumeration we could read, and we do not name them because Owkin does not.
  • No application scopes exist. The RFC 9728 descriptor declares scopes_supported as an empty array, and the Cognito authorization server advertises only openid, email, phone and profile. Nothing at consent separates listing a cohort from exporting one. On a read-only surface the practical gap is narrow — but it is exactly the boundary between the routine read and the bulk export, and it is not offered.
  • We could not read tool schemas or safety annotations. The endpoint returned 401 to an anonymous request, so no parameter detail, readOnlyHint or destructiveHint is published here. The read-only classification is ours, from the names and Owkin's documentation.
  • Sessions last 15 minutes. Owkin states this plainly in its troubleshooting guide, with disconnect-and-reconnect as the remedy. Long analyses will be interrupted.
  • Usage is quota-limited, and the quota is not visible. Owkin's help centre documents a "User quota exceeded" error, states that limits "may reset on a rolling basis", and directs users to contact support to find out when. Owkin adds that it is "working on making usage limits clearer within the platform interface". You cannot check your remaining quota before hitting it.
  • Cohort coverage is TCGA only, and the count is contradictory. 26 cohorts are enumerated; 27 are claimed elsewhere in the same documentation set. No non-TCGA cohort is reachable through this connector.
  • Six cell types, not a general pathology model. Owkin documents lymphocytes, neutrophils, eosinophils, plasmocytes, fibroblasts and cancer cells. Anything outside that set is out of scope.
  • Presigned download URLs are bearer credentials. Anyone with the link can fetch the export without authenticating. Owkin documents the mechanism but publishes no expiry we could find.
  • Permission errors are opaque from the client. Owkin's help centre documents an "Operation not allowed" error covering data outside your subscription and actions outside your account's scope, and its remedies are to rephrase or to contact your Owkin project manager. There is no self-service way to see what your account is permitted.
  • Owkin's terms decline to guarantee non-individualisation. Owkin states it cannot guarantee that outputs consist only of data that never permits individualisation of a patient or research participant. Treat exports as governed research data.
  • The directory's documentation URL redirects. The published value 307s to a different section of Owkin's docs and does not land on the MCP page. The working page is linked below.

Frequently asked questions

How many tools does the Owkin MCP server actually have?

Anthropic's directory lists nine, and Owkin's own changelog says thirteen. The changelog records an initial release of 9 tools on 2025-12-01, 12 tools on 2025-12-31 and 13 tools on 2026-01-15. The directory entry was added 2026-01-12 and still carries the launch set, so treat nine as a stale floor rather than the total.

Can the Owkin connector see my own patient data or uploaded slides?

No. The connector serves TCGA, a public cancer genomics database. Owkin's documentation scopes Pathology Explorer over MCP to TCGA H&E slides only, and the tool names cover cohort listing, slide filtering, feature retrieval, thumbnails and survival analysis. Proprietary data you upload to K Pro is reached through the K Pro platform, not through this connector.

Do I need a paid Claude plan to use the Owkin connector?

Yes, and an Owkin account as well. Owkin's getting-started guide lists three prerequisites: an Owkin account, a paid Claude plan on Pro, Max, Team or Enterprise, and Custom Connectors enabled for your workspace. It states plainly that Claude Free does not support the remote MCP custom connector flow this integration uses.

What OAuth permissions does the Owkin MCP server request?

None that narrow anything. Owkin's RFC 9728 resource descriptor declares scopes_supported as an empty array, and its AWS Cognito authorization server advertises only openid, email, phone and profile — all identity claims. So consent identifies you but draws no boundary between listing a cohort and exporting a whole cohort's features.

Why does my Owkin connection keep dropping in Claude?

Sessions expire after fifteen minutes. Owkin's troubleshooting guide states that sessions currently last 15 minutes and that the fix is to disconnect and reconnect the Owkin connector under Settings then Connectors. That is short enough that a long analysis session will need reconnecting partway through, so expect it rather than treating it as a fault.

Can the Owkin connector write anything back or delete data?

No name in the listing writes or deletes. All nine directory names are reads, renders or exports, and Owkin's own eleven-item tool reference adds only two more read-and-render tile tools. The one outbound path is download_histomics, which Owkin documents as returning a presigned URL for a Parquet download — an export, not a write.

How many TCGA cohorts does Pathology Explorer support?

Owkin's documentation disagrees with itself. Its capabilities page enumerates 26 named cohorts from TCGA_ACC to TCGA_UCS, while its FAQ and glossary both state 27 tumor cohorts. Neither page names the discrepancy. Owkin's own guidance is to ask the connector directly with a prompt requesting the list of available TCGA cohorts.

What does the Owkin connector measure on a histology slide?

Six cell types and the spatial relationships between them. Owkin documents lymphocytes, neutrophils, eosinophils, plasmocytes, fibroblasts and cancer cells, with per-type counts and densities, nuclear morphology, regional densities across tumor, tumor core and stroma, pairwise co-occurrence within 20 micrometres, and a TIL diffusivity metric.

Sources

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