Pluto Bio MCP Connector

Last updated: October 20, 2026

Overview

The Pluto MCP connector lets an AI assistant read and work with Pluto data: programs, datasets, analysis spaces, and plots. It connects to Pluto over the Model Context Protocol (MCP), so you can ask questions in plain language instead of navigating the Pluto interface.

Item	Value
Server URL	https://app.pluto.bio/mcp
Transport	Streamable HTTP (remote)
Authentication	OAuth sign-in with automatic client registration
Access	both read and write
Support	mcp.support@pluto.bio

This page is for Pluto clients. It covers setup for common AI clients, the tools the server exposes, and example prompts.

Connect

Before you start, confirm three things. You have a Pluto account. Your assistant supports custom remote MCP connectors with OAuth sign-in. And, your organization admin has added the connector. Note that your assistant only sees what your Pluto account can see in the organizations you belong to.

Connector settings

Setting	Value	Notes
Name	Pluto Bio	Any name works
URL	https://app.pluto.bio/mcp	Include /mcp at the end
Authentication	OAuth sign-in	Pluto rejects requests without sign-in
OAuth client	Automatic registration (DCR)	Nothing to set up
Headers or API key	Leave empty	Each user's sign-in provides the token
Transport	Streamable HTTP	Pluto does not serve SSE

Admin: add the connector (one time)

Open Organization settings from the profile menu in the bottom-left corner.
Go to Connectors, choose Add, then choose Custom > Web.
Enter Pluto Bio as the name and https://app.pluto.bio/mcp as the URL, then choose Continue.
Keep the detected settings (Sign in now and Register automatically), leave headers empty, and choose Add.

In Claude, skip the other sign-in options. Pluto has no tools that work without an account.

Members: connect your Pluto account

Open your assistant's connector settings and search for Pluto Bio. Do not add a new connector.
Choose Connect. A browser tab opens for Pluto. Sign in if you are not already signed in.
On Pluto's consent screen, check that the return address belongs to your assistant's provider. In Claude, it is https://claude.ai/. If the address is unfamiliar, choose Cancel and contact support (mcp.support@pluto.bio). Otherwise, choose Allow.
In a new chat, open the tools menu in the message box and turn on Pluto Bio. In some cases, the connector will turn on automatically once you connect it, so this step may not be necessary.

Read-only or read and write

The consent screen has a separate checkbox for changes in Pluto. Uncheck it to keep access read-only. Your assistant can still look everything up.

Other AI assistants

Look for a custom or remote MCP connector option in your assistant's settings, then enter the values in the table above. On individual plans, you can usually add the connector yourself.

Authentication and access

The connector acts as you. Each request runs with your Pluto permissions, so you see only the organizations, programs, datasets, and analysis spaces your account can open.

Sign-in uses OAuth with automatic client registration. Your assistant does not need an API key.
Pluto rejects requests that arrive without a sign-in.
Changes made through the connector are logged in your program's History tab as created by you through your AI assistant.
You can approve each tool call one at a time, and you can disconnect at any time.
The default token lifetime is 1hr (configurable), but when it expires, the application using the OAuth tokens has the ability to refresh.

Tools reference

The server exposes the tools below. The first table lists tools that only read data. The second table lists tools that create or change items in Pluto. None of the tools delete data. The only changes to existing items are archiving a plot, which hides it, and renaming clusters in an annotation set. If changes are not allowed for your connection, Pluto refuses the tools in the second table.

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
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
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 and pipeline status
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 an analysis space
get_program_analysis_space_plot_image	Returns the image of one plot

Make changes

Tool	What it does
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:

create_program_analysis_space_plot publishes immediately to everyone who can see the space, with no review step.
create_program_analysis_space_upload sends the file directly to storage, so the machine running the upload needs outbound network access. Hosted sandboxes without it aren’t supported.
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.

Current limitations

Some features are still in development. Check this list before you plan a workflow around the connector.

Gene-level results are not yet available. The connector returns counts of significant genes and pathways, not the gene lists.
Raw counts, normalized matrices, and full sample tables cannot be read yet.
Plot settings cannot be read or changed. Archiving is the only change the connector can make to an existing plot.
Datasets cannot be created or uploaded through the connector
Sample data and cell annotations cannot be edited.
Single-cell preprocessing and differential expression on cell subsets are not available. Cell-level metadata cannot be read.
Uploading results from a hosted AI environment can fail if that environment cannot reach Pluto's cloud storage.
Analysis types vary by dataset. Ask the connector to list the analysis types available for a dataset before you plan a run.

Example prompts

These prompts work once the connector is set up. Replace the names with your own programs and datasets.

"Which Pluto organizations do I belong to?"
"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 lung cancer datasets across my programs."
"Run the suggested next analysis in [analysis space name]."

Common use cases

Plan the next phase of a study by checking which samples come next in a series, without digging through lab notebooks or sample sheets.
Find datasets and analysis spaces across your programs in plain language.
Check what a dataset's sample data contains before you decide how to analyze it.
Upload results from an external analysis into an analysis space, so they stay with the program.

Troubleshooting and support

Common problems

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 that 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 choose Connect again while signed in to Pluto.
A warning icon or Reconnect in your connector list	Your Pluto sign-in expired or was revoked. Choose Reconnect and allow access again.
Your assistant cannot 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 is not allowed to make a change	You declined changes on the consent screen. Disconnect, connect again, and leave the changes box checked.
Pluto Bio is not in your connectors	Your organization has not added it yet. Ask an admin to follow the admin steps above.

For anything else, email mcp.support@pluto.bio and tell us which step it stopped at. Include your client name, the error message, and the time it happened.