Connect your AI assistant to Pluto

Last updated: October 27, 2026

The Pluto Bio connector lets your AI assistant work with your Pluto organizations, programs, datasets, and analysis spaces. Ask a question in plain language and your assistant looks up the answer in Pluto for you.

Server URL: https://app.pluto.bio/mcp

Works with your AI assistant

Pluto's connector is a standard remote MCP (Model Context Protocol) server. It works with any AI assistant that supports custom MCP connectors with sign-in, such as Claude. Menu names differ between assistants, but the settings are the same everywhere. This guide uses Claude for the screenshots and examples.

How setup works

  1. Admin, one time: an admin adds the Pluto Bio connector to your organization's AI workspace. This takes about two minutes.

  2. Every user: each person connects their own Pluto account, then turns Pluto Bio on in a chat.

Before you start

  • You need a Pluto account. Your assistant only sees what your Pluto account can already see, in the organizations you belong to.

  • Your assistant must support custom (remote) MCP connectors with OAuth sign-in.

  • The connector works with your Pluto data.

  • If your organization already has Pluto Bio set up, skip to Connect your Pluto account.

Connector settings

Use these values in any assistant. The steps below show where they go in Claude.

Setting

Use

Why

Name

Pluto Bio

Any name works. This is what appears in your connector list.

URL

https://app.pluto.bio/mcp

Include /mcp at the end.

Authentication

OAuth sign-in, up front

Every Pluto tool needs a Pluto account. Pluto rejects requests without a sign-in.

OAuth client

Automatic registration (DCR)

Pluto supports dynamic client registration. Nothing to set up.

Request headers / API key

Leave empty

Each user's sign-in provides the token. Don't add an Authorization header.

Transport

Streamable HTTP

If your assistant asks. Pluto doesn't serve SSE.

Add the connector (admin, one time)

You only do this once for your organization. After that, members connect with their own Pluto sign-in. Example shown: Claude.

1. Open your organization's settings

In Claude, click your name in the bottom-left corner to open the profile menu, then choose Organization settings.

2. Add a custom connector

Go to Connectors. Click Add, then choose Custom > Web.

3. Name it and paste the URL

Enter Pluto Bio as the name and https://app.pluto.bio/mcp as the URL, then click Continue.

4. Keep the detected settings and click Add

Claude checks the server and marks the options it detects. Pluto's detected options are the right ones: Sign in now and Register automatically. Leave request headers empty, then click Add.

The screenshot shows a test connector name. Yours will say Pluto Bio.

Options to skip in Claude:

  • Sign in when needed and No sign-in: Pluto has no tools that work without an account.

  • Use Claude's published identity: Pluto doesn't support this yet, so the connection would fail.

  • Use your own OAuth client: only needed if Pluto support gave you a client ID.

Using a different assistant, or an individual plan? Look for an option to add a custom or remote MCP connector in your assistant's settings, then enter the values from Connector settings. On individual plans you can usually add the connector for yourself and continue below.

Connect your Pluto account (every user)

Once the connector is added, each user signs in with their own Pluto account.

1. Find Pluto Bio in your connectors

Open your assistant's connector settings and search for Pluto Bio. Use search rather than adding a new connector, since it already exists for your organization.

In Claude: Settings > Connectors, then type Pluto Bio in the search box.

2. Click Connect

On the Pluto Bio connector page, click Connect. A browser tab opens for Pluto.

3. Sign in and allow access

If you're signed out of Pluto, sign in first. You'll then see Pluto's consent screen.

Check that the return address belongs to your AI assistant's provider, then click Allow. If you see an address you don't recognize, click Cancel and contact support.

In Claude, the return address is https://claude.ai/api/mcp/auth_callback.

4. Turn it on in a chat

Back in your assistant, the connector shows as connected. In a new chat, turn on Pluto Bio, then try one of the prompts below.

In Claude: open the tools menu in the message box and switch on Pluto Bio.

Set up in Microsoft Copilot Studio

In Microsoft Copilot Studio, Pluto Bio is added as a Model Context Protocol (MCP) tool on an agent. The first person adds the Pluto Bio server once. After that, anyone in the same Copilot Studio environment can find Pluto Bio in the tool directory and add it to their own agents.

These steps use the classic Copilot Studio experience.

1. Open Copilot Studio

Go to https://copilotstudio.microsoft.com/ and sign in with your Microsoft work account. Check that the Environment in the top-right corner is the one your team uses.

2. Create a blank agent

In the left menu, select Agents, then select Create blank agent.

3. Name the agent

Enter a name for the agent, for example Pluto Bio, then select Create.

4. Add a tool

When the agent page opens, go to the Tools tab and select Add a tool.

If you see This feature isn't available until your agent has finished setting up, wait a minute for setup to finish, then try again.

5. Choose Model Context Protocol

Under Create new, select Model Context Protocol.

6. Enter the Pluto Bio server details

Fill in the form with these values, then select Create.

Field

Enter

Server name

Pluto Bio

Server description

A short description of what Pluto holds, for example Interacting with experimental / omics data sets in Pluto Bio

Server URL

https://app.pluto.bio/mcp (include /mcp at the end)

Authentication

OAuth 2.0

Type

Dynamic discovery

The agent reads the server description to decide when to use Pluto, so describe the data rather than the company.

Don't choose None or API key. Pluto rejects requests without a sign-in. Dynamic discovery uses Pluto's automatic client registration, so you don't need a client ID or secret.

7. Connect your Pluto account

Copilot Studio asks you to create a connection to Pluto Bio. After you confirm, a browser tab opens for Pluto. Sign in if you're signed out, then review Pluto's consent screen.

Check that the return address belongs to Microsoft, then select Allow. If you see an address you don't recognize, select Cancel and contact support.

When the connection works, the Connection field on the tool page shows Pluto Bio connector with a green check.

8. Review the tools and test your agent

Once the tool is added, its page lists every Pluto tool the agent can use. Each tool has its own switch, so you can turn off the tools that create things if you want this agent to stay read-only.

Use the Test your agent panel on the right to chat with Pluto. Try Summarize my programs in Pluto or one of the prompts below.

Add Pluto Bio to another agent

You only enter the server details once per environment. To use Pluto in another agent, or for a teammate to add it to their own agent:

  1. Open the agent and go to Tools > Add a tool.

  2. Search for pluto and filter by Model Context Protocol.

  3. Select Pluto Bio, then connect your own Pluto account as in step 7.

Each person signs in with their own Pluto account, so the agent only sees what that person can see in Pluto.

Read-only or read and write

You decide whether your assistant can make changes in Pluto.

On the consent screen: a separate checkbox asks whether the assistant may make changes in Pluto. Uncheck it to keep access read-only. Your assistant can still look everything up.

The first time each tool runs: most assistants ask before using a tool. Allowing lookup tools every time is reasonable. For the three tools that create things, approve each use so you can review the change first. In Claude these choices are Allow once and Always allow.

You can usually change these choices later in the connector's settings. None of the Pluto tools delete or overwrite anything.

Prompts to try

Start with the first one. The others build on it, and your assistant finds the IDs it needs on its own.

  • Which Pluto organizations do I belong to?

  • List the programs in [your organization], 5 at a time, and show me the second page.

  • Pick one of those programs and summarize its datasets and analysis spaces.

  • Open the first dataset in that program and tell me its organism and pipeline status.

  • Find any NSCLC datasets across my programs.

What your assistant can do

Look things up

Tool

What it does

whoami

Shows which Pluto account results are scoped to

list_organizations

Lists the organizations you belong to. Your assistant starts here.

list_programs

Lists one page of programs in an organization, searchable

get_program

Returns one program's summary

list_program_datasets

Lists the datasets linked to a program, filterable by assay, organism, tissue, cell type or disease

get_program_dataset

Returns one dataset by UUID or Pluto ID

get_program_dataset_sample_data_profile

Returns a profile of a dataset's sample data: groups, replicates and the likely grouping column

get_program_dataset_sample_data

Reads a dataset's full sample table, one row per sample

get_program_dataset_assay_data

Reads a bulk dataset's assay data, as uploaded or as counts per million, for all genes and samples or only the ones you name

list_organization_dataset_types

Lists the dataset types your organization can create from tables, with their organisms and units

get_program_dataset_cell_annotation

For a single-cell dataset, lists its clustering resolutions and annotation sets

get_program_dataset_cluster_markers

Returns the marker genes for each cluster

list_program_dataset_analysis_types

Lists the analysis types available on a dataset or analysis space

get_program_dataset_analysis_type

Returns one analysis type and what it takes

get_program_dataset_analysis

Returns one analysis with its parameters, pipeline status and counts of significant results

get_program_dataset_analysis_results

Reads the full results table of a completed analysis, such as differential expression or gene set enrichment, filterable by p-value, effect size or gene

list_program_analysis_spaces

Lists a program's analysis spaces

get_program_analysis_space

Returns one analysis space by UUID or Pluto ID

list_program_analysis_space_datasets

Lists the datasets linked into an analysis space

list_program_analysis_space_analyses

Lists the analyses in an analysis space

list_program_plots

Lists the plots in a program or analysis space

get_program_analysis_space_plot_image

Returns the image of one plot

Make changes

Tool

What it does

create_program_dataset

Creates an empty draft dataset in a program, of a type and organism your organization offers

create_program_dataset_upload

Prepares an upload of a dataset's assay data or sample data table (CSV, up to 500 MB)

update_program_dataset_data

Loads an uploaded table into a dataset, replacing its assay data or sample data. Pluto then processes it.

create_program_analysis_space

Creates an analysis space in a program

create_program_analysis_space_datasets

Links datasets into an analysis space

create_program_analysis_space_upload

Prepares an upload of a result file for a new analysis

create_program_analysis_space_analysis

Creates an analysis in an analysis space from uploaded files

create_program_analysis_space_plot

Runs an analysis on a dataset or analysis space and adds its plot to the space

create_program_analysis_space_plot_link

Draws an arrow between two plots on a space's canvas

create_program_analysis_space_canvas_plot

Draws one of a space's plots on its canvas

update_program_analysis_space_plot

Archives a plot in an analysis space, which hides it. A person can restore it in Pluto.

create_program_dataset_annotation_set

Creates an annotation set from a single-cell dataset's clusters

update_program_dataset_annotation_set

Renames clusters in an annotation set

create_program_dataset_cell_groups

Splits a single-cell dataset's cells into groups by sample variables, clusters or latent variables

create_program_dataset_comparison_groups

Splits a dataset's samples into groups by one or more variables

A few notes to consider about a subset of tools:

  • update_program_dataset_data replaces the dataset's existing assay or sample table for everyone who can see the dataset. Pluto validates and processes the new table, usually within minutes.

  • create_program_dataset_upload and create_program_analysis_space_upload send the file directly to storage, so the machine running the upload needs outbound network access. Hosted sandboxes without it aren't supported.

  • Large reads from get_program_dataset_assay_data, get_program_dataset_sample_data and get_program_dataset_analysis_results come back as a download link instead of rows in the chat.

  • create_program_analysis_space_plot publishes immediately to everyone who can see the space, with no review step.

  • create_program_analysis_space_datasets takes dataset UUIDs, not Pluto IDs.

  • update_program_dataset_annotation_set renames clusters for everyone at once, so it should run only after the user agrees to the names.

  • update_program_analysis_space_plot can only archive a plot, not restore it.

Troubleshooting

What you see

What to do

Connect does nothing, or fails right away

Ask your admin to check that the URL is exactly https://app.pluto.bio/mcp and the OAuth client uses automatic registration. If not, remove the connector and add it again.

After sign-in you land in the Pluto web app, not the consent screen

Close the tab and click Connect again while signed in to Pluto.

A warning icon or Reconnect in your connector list

Your Pluto sign-in expired or was revoked. Click Reconnect and allow access again.

Your assistant can't see a program you know exists

Ask it which organization it used. It sees only what your account can see, one organization at a time.

Your assistant says it isn't allowed to make a change

You declined changes on the consent screen. Disconnect, connect again, and leave the changes box checked.

Pluto Bio doesn't show up in your connectors

Your organization hasn't added it yet. Ask an admin to follow Add the connector.

Anything else

Email mcp.support@pluto.bio and tell us which step it stopped at.