Micro-Manager Microscope MCP Server

Let an AI agent snap images, acquire z-stacks and time-lapses, move the stage and focus within limits you set, switch channels and objectives, set exposure, operate shutters and run autofocus on any microscope controlled by Micro-Manager, through its open device layer (MMCore) and pymmcore-plus. Its 19 documented tools cover acquire, shutter, exposure, stage.

People who work with acquire, shutter and exposure and want it reachable from Claude, Cursor, VS Code, or another MCP client. The project is written in Python.

One of 32 MCP servers published from k-dense-ai/lab-instrument-mcps. Stars and repository activity are shared across all of them. See all 32 →

VERIFIED ACTIVE

LAST COMMIT 2026-09-26 · VERIFIED 2026-09-30

Apache-2.0 · Python servers · how we verify → /methodology

01 · Install Micro-Manager Microscope

Claude Code

claude mcp add k-dense-ai-lab-instrument-mcps-servers-b -- uvx labmcp-micro-manager

Claude Desktop / Cursor / VS Code - add to config

{
  "mcpServers": {
    "k-dense-ai-lab-instrument-mcps-servers-b": {
      "command": "uvx",
      "args": [
        "labmcp-micro-manager"
      ]
    }
  }
}

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions

repo age created 2026-09-25 - young repo, little track record yet

license Apache-2.0 - declared in the repository

pypi package labmcp-micro-manager - check the name against the project README before installing (PyPI has no namespace ownership)

registry namespace io.github.K-Dense-AI is GitHub-verified and matches the repo owner

03 · What Micro-Manager Microscope can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

What you can build

g. a hardware focus lock) once, close the shutter (stop illuminating the sample) and abort any running acquisition, read the camera exposure time in milliseconds, and read the XY stage and focus (Z) positions in micrometres, and which way increasing Z moves the objective.

Capability map

Tools grouped from the project's README - what Micro-Manager Microscope lets an agent do.

read & search

4 tools - e.g. Return the most recent raw commands sent to / replies received from the instrument (newest last). Useful for debugging and for recording what was done.; Report which instrument is connected (identity…

get_command_log · get_connection_info · get_position · get_system_info

update

3 tools - e.g. Move the focus drive (Z). Moving the objective toward the sample can crash it into the slide: moves larger than max_z_step_um or outside the Z soft limits are r; Switch the objective (rotates the…

move_z · set_objective · set_shutter

Acquire

2 tools - e.g. Acquire a time-lapse at the current position: images every interval_s (optionally several channels per timepoint), saves a multi-page TIFF and reports per-frame; Acquire a z-stack around the current…

acquire_time_lapse · acquire_z_stack

Exposure

2 tools - e.g. Return the camera exposure time in milliseconds.; Set the camera exposure time (ms). Longer exposures give brighter images but more photobleaching. Returns the exposure the camera accepted.

get_exposure · set_exposure

Config

2 tools - e.g. List Micro-Manager config groups (e.g. Channel, Objective) with their presets and the preset currently active.; Apply a config-group preset (e.g. switch the channel: filter cube, light source, emission…

list_config_groups · set_config

Stage

2 tools - e.g. Move the XY stage. Moves longer than max_xy_step_um or outside the XY soft limits are refused before anything moves. Make sure the objective and condenser clear; Immediately stop XY and Z stage motion and…

move_stage_xy · stop_stage

Autofocus

1 tool - e.g. Run the configured autofocus device (e.g. a hardware focus lock) once; it moves the focus drive. If the result is outside the Z step or soft limits, the focus i

autofocus

1 tool - e.g. Close the shutter (stop illuminating the sample) and abort any running acquisition.

close_shutter

Limitations (from the README)

- Objective crashes. Moving the focus drive toward the sample can drive the objective into the coverslip or dish. get_position / get_system_info report focus_direction (whether increasing Z moves the objective toward the sample, as declared by the device adapter; often unknown). Configure z_min_um / z_max_um for every microscope you connect. - Objective changes (set_objective) rotate the nosepiece and are marked as h

04 · Who maintains Micro-Manager Microscope

Micro-Manager Microscope is maintained by k-dense-ai. We track 32 MCP servers from k-dense-ai - 32 actively maintained, 9 combined GitHub stars, oldest repo from Sep 2026. Full record: all servers from k-dense-ai.

05 · Facts

repository: github.com/k-dense-ai/lab-instrument-mcps
website: https://github.com/K-Dense-AI/lab-instrument-mcps/tree/main/servers/biology/micro-manager
category: other - actively maintained as of 2026-09-30.
registry: io.github.K-Dense-AI/labmcp-micro-manager (active, first published 2026-09-25 · 4 versions)
packages: pypi:labmcp-micro-manager

06 · Micro-Manager Microscope FAQ

Is Micro-Manager Microscope still maintained?

Yes - as of 2026-09-30, its last commit was 2026-09-26. We re-verify nightly.

What can Micro-Manager Microscope do?

How do I install Micro-Manager Microscope?

Run `uvx labmcp-micro-manager`. You can also paste the ready-made client config above.

Does Micro-Manager Microscope run locally?

Yes - it's a stdio server: it runs on your machine (via uvx) with your user's permissions. Your data stays local unless the server itself calls external APIs.

07 · Alternatives to Micro-Manager Microscope

Alternatives to Micro-Manager Microscope

Maintained other servers if Micro-Manager Microscope isn't the fit.

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