It records the command and runtime settings required for the server to start correctly on that machine.

cellpose — MCP server by surajinacademia/cellpose

cellpose

cellpose is an MCP server for Claude Code, Codex, Cursor, Gemini CLI, OpenCode from surajinacademia/cellpose_mcp. Its token cost is not measured, scanned A, original, BSD-3-Clause.

An MCP server configuration for Cellpose, a tool used to identify cells in scientific images. It starts the Cellpose MCP program with a specific Python interpreter and environment settings.

In plain words

What is it for?: Connecting an MCP-compatible coding agent to Cellpose for cell-image analysis, when the listed Python environment and variables are available.
Why use it?: It records the command and runtime settings required for the server to start correctly on that machine.

Written for no agent in particular: it speaks MCP, so any client can run it. Also seen: listed in a Claude config.

Not installable: its command points at a path on the author’s own machine, so it runs nowhere else. The line is /Users/suraj/miniconda3/bin/python.

One of 2 entries in .mcp.json upstream. Installing this one merges just its entry into your config; the other 1 are separate, each on its own page.

Good fit Connecting an MCP-compatible coding agent to Cellpose for cell-image analysis, when the listed Python environment and variables are available.

Compare 6 mcp servers from other repositories ↓

Installing this writes the configuration, not the program: `python` runs a file from the repository, so clone it first and make the path in the command match where you put it.

Install

Getting it into your agent

There is no command for this one: it runs only inside a plugin, and the catalogue could not identify which plugin ships it. The source is linked below.

Installing this writes the configuration, not the program: `python` runs a file from the repository, so clone it first and make the path in the command match where you put it.

Made for: Claude Code, Codex, Cursor, Gemini CLI, OpenCode.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/mcp/surajinacademia/cellpose_mcp/cellpose/github.svg)](https://agentmods.dev/mcp/surajinacademia/cellpose_mcp/cellpose)

Your own site

<a href="https://agentmods.dev/mcp/surajinacademia/cellpose_mcp/cellpose"><img src="https://agentmods.dev/badge/mcp/surajinacademia/cellpose_mcp/cellpose/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/mcp/surajinacademia/cellpose_mcp/cellpose"><img src="https://agentmods.dev/badge/mcp/surajinacademia/cellpose_mcp/cellpose.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session not measured What this adds to a session before it is invoked.

When invoked not measured Not applicable: nothing here is loaded into a session.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Security

Grade A, and why

cellpose scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.mcp.json · 13 lines

What it actually says

{
  "cellpose": {
    "command": "/Users/suraj/miniconda3/bin/python",
    "args": [
      "-m",
      "cellpose_mcp"
    ],
    "env": {
      "KMP_DUPLICATE_LIB_OK": "TRUE",
      "OMP_NUM_THREADS": "1"
    }
  }
}

Same file

What else `.mcp.json` configures

This page is one entry in a file that holds 2. Installing the file brings all of them; each is measured and scanned on its own page.

MCP server ppt A not measured

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

2mo ago First seen · 13 lines scan A 1963b4371637

Subscribe to this mod's changes

cellpose is an MCP server published in the GitHub repository surajinacademia/cellpose_mcp (2 stars, last pushed 2mo ago), licensed BSD-3-Clause. Its token cost is not measured: an MCP server costs its tool schemas, not its config file. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

Scientific cell-biology image-analysis-workflows

cellpose next to 6 mcp servers from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
cellposesurajinacademia/cellpose_mcp	MCP server	2	2mo ago	BSD-3-Clause	A	—	Claude Code, Codex, Cursor, Gemini CLI, OpenCode
health-system-profilerajhcs/healthcare-data-mcp	MCP server	9	1mo ago	MIT	A	—	Claude Code, Codex, Cursor, Gemini CLI, OpenCode
clinical-trials-ai-mcpCSOAI-ORG/clinical-trials-ai-mcp	MCP server	0	1mo ago	MIT	A	—	Claude Code, Codex, Cursor, Gemini CLI, OpenCode
outdooriq-mcpbch1212/outdooriq-mcp	MCP server	0	1mo ago	MIT	A	—	Claude Code, Codex, Cursor, Gemini CLI, OpenCode
mcp-airqCorantGmbH/mcp-airq	MCP server	0	3mo ago	Apache-2.0	A	—	Claude Code, Codex, Cursor, Gemini CLI, OpenCode
mcp-sympydaedalus/mcp-sympy	MCP server	0	6mo ago	MIT	A	—	Claude Code, Codex, Cursor, Gemini CLI, OpenCode
weather-mcp-agentShivbaj/MCP	MCP server	0	1y ago	MIT	A	—	Claude Code, Codex, Cursor, Gemini CLI, OpenCode