SkillFoxx

SP-Mind plugin

SP-Mind is a Claude Agent SDK agent for spatial proteomics analysis: from image correction to cell type annotation.

  • 280 ★ on the repository
  • Last commit
  • Apache-2.0
Plugin

Extended access

Why this level

  • The agent writes and runs code and `--sandbox` blocks destructive commands.
  • Work runs on an Anthropic key and containers, with costs on the user.
All reasons and checks

tomtommyyuan/spmindAuthor:tomtommyyuan

Install

Works in

In your terminal, with SkillFoxx CLI

npx skillfoxx add plugins/sp-mind

Detects the agents on your machine, shows the access level and pins the version.

Other ways to install

Access and checks

How we review

Extended accessThe tool runs code or makes network calls and only reads external data.

  • The agent writes and runs code and `--sandbox` blocks destructive commands.
  • Work runs on an Anthropic key and containers, with costs on the user.

This is third-party code. Review the repository files before installing.

What it does

SP-Mind is a research agent accompanying an ICML 2026 paper. It selects tools, writes code, inspects intermediate results and repeats the loop. Underneath are containers with the usual multiplexed imaging toolchain: BaSiC illumination correction, ASHLAR registration, background subtraction, UnMICST nuclei detection, S3Segmenter segmentation, MCQuant quantification and Scimap clustering. Cell type annotation is guided by skills with methods for each stage. The `--mcp` mode exposes the full toolset as an MCP server installable in Claude Desktop or Claude Code and `--sandbox` installs `PreToolUse` guardrails. The repository includes SP-Bench, a task set for evaluation.

Who it is for. Bioinformaticians and tumor microenvironment researchers analyzing spatial proteomics images who want an agent to run the processing chain.

Good fit when

  • Multiplexed imaging must go from illumination correction to a quantification table.
  • Cell types should be assigned from markers and stage methods.
  • The toolset should be attached to Claude Code as MCP.
  • Agents are to be compared on SP-Bench tasks.

Not a fit when

  • You need a clinical conclusion: results are checked by a specialist.
  • Docker, Apptainer or Singularity is missing for the tool containers.
  • The data is not spatial proteomics but another field.

Example request

Run the sample images from illumination correction to segmentation and a quantification table, then propose cell types from markers.

Limitations

The project is for research, results do not replace a specialist's review and are not for clinical decisions. Python 3.11 or newer, the Claude Code CLI, Docker or Apptainer and an `ANTHROPIC_API_KEY` are required, and costs on the key are yours. Tool containers must be pulled with scripts from `scripts/`. Installing `scimap` separately comes with caveats about outdated dependency versions. `--mcp` mode is off by default. The last commit is from October 2026.

How to disable. Remove the package with `pip uninstall spmind`, the MCP entry from the client and the pulled containers. Delete the repository folder manually.

FAQ

What is needed to install?

Python 3.11 or newer, the Claude Code CLI, Docker or Apptainer and an `ANTHROPIC_API_KEY`.

How do I pull the containers?

With scripts: `scripts/pull_docker_images.sh` for Linux and Intel Mac, an ARM64 variant and an Apptainer script.

What does `--sandbox` do?

Installs `PreToolUse` guardrails that block destructive shell commands before they run.

How do I use it inside Claude?

`--mcp` mode exposes tools as an MCP server with typed schemas that can be installed in Claude Desktop or Claude Code.

What is SP-Bench?

A set of realistic spatial proteomics queries with scripts evaluating annotation and quantification.

Discussion

No questions or reviews yet.

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README in short

The README includes the paper abstract, an agent overview, a stage table with tools, installation, quick start and modes. A 55-second video overview is linked.

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