Micro-Manager Microscope
PYPI · LABMCP-MICRO-MANAGER · SCANNED SEP 30
MCP server for microscopes controlled by Micro-Manager (pymmcore-plus).
Available components
How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. How we score → Why this is hard to score →
Supply Chain Security49
- Malware scan not yet available for this package.Unverified
- No known CVEs affecting this package version or its production dependencies.Pass
- Runs hatchling.build at install time, a recognised build step with no custom scripting around it. View diagnostics → Pass
- 4 of 34 dependencies flagged as unhealthy. View diagnostics → Partial
Provenance & Transparency100
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Cryptographically verified build provenance (signed, bound to K-Dense-AI/lab-instrument-mcps). View diagnostics → Pass
- Clear OSI-approved license (Apache-2.0).Pass
- Actively maintained (last published 3 days ago).Pass
- Publishes a security disclosure policy (SECURITY.md).Pass
Schema Quality & AI Usability78
- AI-judged instruction clarity (excellent).Pass
- Tool/resource definitions use about 1769 tokens (~93/item across 19 items; 19 tools + 0 resources), lean.Pass
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management17
- Stability observed for 5 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage99
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 97% of tool parameters carry a description.Partial
- Structured output schemas are declared (100% of tools); any adoption earns full credit.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 19 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 20 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a current MCP spec version (2026-07-28).Pass
How do I install the Micro-Manager Microscope MCP server?
Micro-Manager Microscope runs locally as a PyPI package, launched with uvx labmcp-micro-manager. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
pypi · labmcp-micro-manager
claude mcp add k-dense-ai-labmcp-micro-manager -- uvx labmcp-micro-manager
{
"mcpServers": {
"k-dense-ai-labmcp-micro-manager": {
"command": "uvx",
"args": [
"labmcp-micro-manager"
]
}
}
} {
"servers": {
"k-dense-ai-labmcp-micro-manager": {
"command": "uvx",
"args": [
"labmcp-micro-manager"
]
}
}
} codex mcp add k-dense-ai-labmcp-micro-manager -- uvx labmcp-micro-manager
{
"$schema": "https://opencode.ai/config.json",
"mcp": {
"k-dense-ai-labmcp-micro-manager": {
"type": "local",
"command": [
"uvx",
"labmcp-micro-manager"
],
"enabled": true
}
}
} openclaw mcp add k-dense-ai-labmcp-micro-manager --command uvx --arg labmcp-micro-manager
mcp_servers:
k-dense-ai-labmcp-micro-manager:
command: "uvx"
args: ["labmcp-micro-manager"] {
"McpServers": {
"k-dense-ai-labmcp-micro-manager": {
"Transport": "stdio",
"Command": "uvx",
"Arguments": [
"labmcp-micro-manager"
]
}
}
} assistant mcp add k-dense-ai-labmcp-micro-manager -t stdio -c uvx -a labmcp-micro-manager
{
"mcpServers": {
"k-dense-ai-labmcp-micro-manager": {
"command": "uvx",
"args": [
"labmcp-micro-manager"
]
}
}
} Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 30 Sept 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 13 to 17. That category is still filling its 30-day observation window: 4 days of observed history at the previous scan, 5 at this one. The score rises as the window fills, whether or not the server changes.
- 28 Sept 26 +29
- We updated how we score, so this day's move reflects our rubric, not a change to the server See what changed → functional
- 27 Sept 26 0
- Package version: 0.1.2 → 0.1.3 functional
- 26 Sept 26 −17
- Tool safety: pass → unverified ▼ security
- Malware scan: unverified → pass ▲ security
- Stability: Stability not yet verified: we do not have a sandbox capture of the MCP schema this version of the package serves yet. security
- Capabilities: pass → unverified ▼ functional
- Tool coverage: 100 → unverified ▼ functional
- Stability: unverified → 0.03 ▲ functional
- First check of Schema quality: unverified functional
- Package version: 0.1.0 → 0.1.2 functional
- Package version: 0.1.0 → 0.1.1 functional
- 25 Sept 26 56
First indexed and scored.
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 30 Sept 2026 · Analysed pypi/labmcp-micro-manager@0.1.3
Provenance Verified
A signed build attestation was found and verified, binding this exact artifact to the source repository it claims to come from.
| Result | Verified |
|---|---|
| Ecosystem | pypi |
| Reason | Verified |
| Discovered via | Registry attestation endpoint |
| Source repo | K-Dense-AI/lab-instrument-mcps |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/K-Dense-AI/lab-instrument-mcps/.github/workflows/release.yml@refs/tags/labmcp-micro-manager-v0.1.3 |
| Rekor log index | 2969516658 |
| Predicate type | PyPI publish attestation https://docs.pypi.org/attestations/publish/v1 |
| Subject digest | sha256:722500eb309e6ea6f6d57118ae7356387ab21c659617abc35581dd757278ad5a |
Background: How many MCP packages publish verified provenance →
Install scripts 1 script
| Hook | Tier | Command |
|---|---|---|
| build_backend | allowlisted | hatchling.build |
Background: Why install scripts are a supply-chain risk →
Dependencies 34 packages
| Packages resolved | 34 |
|---|---|
| Stale | 4 |
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
acquire_time_lapse Acquire Time Lapse ~172
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 statistics and the intensity change (bleaching). Bounded by `max_frames` and `max_acquisition_duration_s`; `stop_stage` aborts it.
| Name | Type | Req | Description |
|---|---|---|---|
| channel_group | – | – | Config group of the channels; default: channel group |
| channels | – | – | Channel presets to image at every timepoint; omit for current settings |
| include_preview | boolean | – | Return a preview of the last frame |
| interval_s | number | yes | Time between timepoint starts (s) |
| save_path | – | – | Multi-page TIFF path (ImageJ hyperstack, TCYX) |
| timepoints | integer | yes | Number of timepoints |
| Name | Type | Req | Description |
|---|---|---|---|
| aborted | boolean | yes | – |
| axes | string | yes | – |
| channels | array | yes | – |
| duration_s | number | yes | – |
| frames | array | yes | Per-frame statistics (at most 100 evenly spaced frames) |
| intensity_change_percent | object | yes | Mean intensity change from first to last timepoint per channel (bleaching/drift indicator) |
| interval_s | number | yes | – |
| note | – | – | Why the acquisition ended early, if it did |
| path | string | yes | – |
| shape | array | yes | – |
| timestamp | string | yes | – |
No examples provided.
acquire_z_stack Acquire Z Stack ~207
Acquire a z-stack around the current focus: moves Z through the slices (optionally imaging several channels at each), saves a multi-page TIFF, reports per-slice statistics and the sharpest slice, and returns Z to where it started. Every slice must stay within `max_z_step_um` of the start and the Z soft limits.
| Name | Type | Req | Description |
|---|---|---|---|
| channel_group | – | – | Config group of the channels; default: channel group |
| channels | – | – | Channel presets to image at every slice; omit for current settings |
| end_offset_um | number | yes | Last slice relative to the current Z (e.g. +10) |
| include_preview | boolean | – | Return a max-intensity projection preview |
| save_path | – | – | Multi-page TIFF path (ImageJ hyperstack, ZCYX) |
| start_offset_um | number | yes | First slice relative to the current Z (e.g. -10) |
| step_um | number | yes | Spacing between slices (µm) |
| Name | Type | Req | Description |
|---|---|---|---|
| aborted | boolean | yes | – |
| axes | string | yes | Axis order of the TIFF, e.g. 'ZCYX' |
| best_focus_z_um | – | yes | Z of the sharpest slice (first channel) |
| channels | array | yes | – |
| duration_s | number | yes | – |
| frames | array | yes | – |
| note | – | – | Why the acquisition ended early, if it did |
| path | string | yes | – |
| returned_to_z_um | – | yes | – |
| shape | array | yes | – |
| timestamp | string | yes | – |
| z_positions_um | array | yes | – |
No examples provided.
autofocus Autofocus ~52
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 is moved back and an error is raised.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| moved_um | number | yes | Distance moved |
| timestamp | string | yes | – |
| toward_sample | – | – | For Z moves: True if the objective moved toward the sample |
| x_um | – | yes | – |
| y_um | – | yes | – |
| z_um | – | yes | – |
No examples provided.
close_shutter Close Shutter ~24
Close the shutter (stop illuminating the sample) and abort any running acquisition.
Input schema present but exposes no named parameters.
Structured output declared, but exposes no named fields.
No examples provided.
get_command_log Get Command Log ~46
Return the most recent raw commands sent to / replies received from the instrument (newest last). Useful for debugging and for recording what was done.
| Name | Type | Req | Description |
|---|---|---|---|
| limit | integer | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| result | array | yes | – |
No examples provided.
get_connection_info Get Connection Info ~40
Report which instrument is connected (identity, address, simulated or real), whether the server is read-only, and the active safety limits. Call this first.
Input schema present but exposes no named parameters.
Structured output declared, but exposes no named fields.
No examples provided.
get_exposure Get Exposure ~17
Return the camera exposure time in milliseconds.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| result | number | yes | – |
No examples provided.
get_position Get Position ~34
Read the XY stage and focus (Z) positions in micrometres, and which way increasing Z moves the objective.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| focus | – | yes | – |
| focus_direction | string | yes | What increasing Z does: 'toward_sample', 'away_from_sample' or 'unknown' |
| timestamp | string | yes | – |
| x_um | – | yes | – |
| xy_stage | – | yes | – |
| y_um | – | yes | – |
| z_um | – | yes | – |
No examples provided.
get_system_info Get System Info ~64
Describe the microscope: loaded devices (camera, stages, shutters, filter wheels...), which device has which role, camera size/bit depth/exposure, pixel size, config groups with their presets, the current position, and the soft limits. Call this first.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| auto_shutter | boolean | yes | – |
| autofocus | – | yes | – |
| bit_depth | – | yes | – |
| camera | – | yes | – |
| config_groups | array | yes | – |
| configuration | string | yes | – |
| devices | array | yes | – |
| exposure_ms | – | yes | – |
| focus | – | yes | – |
| image_height_px | – | yes | – |
| image_width_px | – | yes | – |
| mmcore_version | string | yes | – |
| pixel_size_um | – | yes | Calibrated pixel size for the current objective, if configured |
| position | object | yes | – |
| shutter | – | yes | – |
| shutter_open | – | yes | – |
| soft_limits_um | object | yes | – |
| timestamp | string | yes | – |
| xy_stage | – | yes | – |
No examples provided.
list_config_groups List Config Groups ~33
List Micro-Manager config groups (e.g. Channel, Objective) with their presets and the preset currently active.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| result | array | yes | – |
No examples provided.
move_stage_xy Move Stage Xy ~107
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 the sample holder.
| Name | Type | Req | Description |
|---|---|---|---|
| relative | boolean | – | Interpret x_um/y_um as offsets from the current position |
| x_um | number | yes | Target X (µm), or the X offset if relative=True |
| y_um | number | yes | Target Y (µm), or the Y offset if relative=True |
| Name | Type | Req | Description |
|---|---|---|---|
| moved_um | number | yes | Distance moved |
| timestamp | string | yes | – |
| toward_sample | – | – | For Z moves: True if the objective moved toward the sample |
| x_um | – | yes | – |
| y_um | – | yes | – |
| z_um | – | yes | – |
No examples provided.
move_z Move Z ~87
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 refused before anything moves.
| Name | Type | Req | Description |
|---|---|---|---|
| relative | boolean | – | Interpret z_um as an offset from the current position |
| z_um | number | yes | Target focus position (µm), or the offset if relative=True |
| Name | Type | Req | Description |
|---|---|---|---|
| moved_um | number | yes | Distance moved |
| timestamp | string | yes | – |
| toward_sample | – | – | For Z moves: True if the objective moved toward the sample |
| x_um | – | yes | – |
| y_um | – | yes | – |
| z_um | – | yes | – |
No examples provided.
reconnect Reconnect ~35
Close and re-open the connection to the instrument (e.g. after it was power cycled or a cable was re-plugged).
Input schema present but exposes no named parameters.
Structured output declared, but exposes no named fields.
No examples provided.
set_config Set Config ~80
Apply a config-group preset (e.g. switch the channel: filter cube, light source, emission filter). Objective/turret groups are refused here: use `set_objective`.
| Name | Type | Req | Description |
|---|---|---|---|
| group | string | yes | Config group, e.g. 'Channel' |
| preset | string | yes | Preset in that group, e.g. 'FITC' |
| Name | Type | Req | Description |
|---|---|---|---|
| current | – | yes | – |
| name | string | yes | – |
| presets | array | yes | – |
| role | – | yes | 'channel', 'objective' or None |
No examples provided.
set_exposure Set Exposure ~49
Set the camera exposure time (ms). Longer exposures give brighter images but more photobleaching. Returns the exposure the camera accepted.
| Name | Type | Req | Description |
|---|---|---|---|
| exposure_ms | number | yes | Camera exposure time in ms |
| Name | Type | Req | Description |
|---|---|---|---|
| result | number | yes | – |
No examples provided.
set_objective Set Objective ~82
Switch the objective (rotates the nosepiece/turret). A longer or immersion objective can hit the sample holder or need oil/water: confirm with the user first. Pixel size changes with the objective.
| Name | Type | Req | Description |
|---|---|---|---|
| group | – | – | Objective config group; default: auto-detected |
| preset | string | yes | Objective preset, e.g. '20x' |
| Name | Type | Req | Description |
|---|---|---|---|
| current | – | yes | – |
| name | string | yes | – |
| presets | array | yes | – |
| role | – | yes | 'channel', 'objective' or None |
No examples provided.
set_shutter Set Shutter ~79
Open or close the current shutter, and optionally switch auto-shutter. An open shutter illuminates (and bleaches) the sample until it is closed again.
| Name | Type | Req | Description |
|---|---|---|---|
| auto_shutter | – | – | Also set auto-shutter (open only during exposures). Leave on normally. |
| open | boolean | yes | True opens the shutter (sample illuminated continuously) |
Structured output declared, but exposes no named fields.
No examples provided.
snap_image Snap Image ~110
Acquire one image with the current channel, exposure and position. The sample is illuminated during the exposure. Saves the full image as TIFF and returns summary statistics (min/max/mean, saturation, sharpness) plus an optional contrast-stretched preview.
| Name | Type | Req | Description |
|---|---|---|---|
| include_preview | boolean | – | Return a small PNG preview image |
| preview_size_px | integer | – | Longest side of the preview |
| save_path | – | – | TIFF path for the full image; default: a timestamped file in data_dir |
| Name | Type | Req | Description |
|---|---|---|---|
| bit_depth | integer | yes | – |
| dtype | string | yes | – |
| exposure_ms | number | yes | – |
| focus_score | number | yes | Sharpness (normalised gradient energy); compare within one field |
| height_px | integer | yes | – |
| max | number | yes | – |
| mean | number | yes | – |
| min | number | yes | – |
| path | string | yes | TIFF file with the full image |
| pixel_size_um | – | yes | – |
| presets | object | yes | Current preset of every config group |
| saturated_fraction | number | yes | Fraction of pixels at the camera's maximum value |
| std | number | yes | – |
| timestamp | string | yes | – |
| warning | – | yes | – |
| width_px | integer | yes | – |
| x_um | – | yes | – |
| y_um | – | yes | – |
| z_um | – | yes | – |
No examples provided.
stop_stage Stop Stage ~27
Immediately stop XY and Z stage motion and abort any z-stack or time-lapse in progress.
Input schema present but exposes no named parameters.
Structured output declared, but exposes no named fields.
No examples provided.
What is the Micro-Manager Microscope MCP server?
Micro-Manager Microscope is an MCP server listed in the public MCP registry as io.github.K-Dense-AI/labmcp-micro-manager. MCP server for microscopes controlled by Micro-Manager (pymmcore-plus). This page covers its PyPI package (labmcp-micro-manager).
Is the Micro-Manager Microscope MCP server safe to use?
Micro-Manager Microscope scores 69 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 30 September 2026. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the Micro-Manager Microscope MCP server expose?
Micro-Manager Microscope exposes 19 tools: get_connection_info, get_command_log, reconnect, get_system_info, list_config_groups, and 14 more. Their descriptions and schemas cost roughly 1,345 tokens of context every time the server is loaded.
Is the Micro-Manager Microscope MCP server still maintained?
Micro-Manager Microscope is still listed as active in the MCP registry. We last reached this channel on 30 September 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.
What licence is the Micro-Manager Microscope MCP server under?
Micro-Manager Microscope declares the Apache-2.0 licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.