New: 97,000+ skills indexed from GitHub repos with 100+ stars · every skill safety-checkedBrowse top skillsTop skills
Esc to closeBrowse all skills
Submit a skillBrowse skills
Submit a skillBrowse skills

Agent skill

Bio Spatial Transcriptomics Spatial Proteomics

by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills

Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization.

No licenceAuto-check passedResearch & Science

Install Bio Spatial Transcriptomics Spatial Proteomics

skills CLI
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-proteomics -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-spatial-transcriptomics-spatial-proteomics --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-spatial-transcriptomics-spatial-proteomics .claude/skills/bio-spatial-transcriptomics-spatial-proteomics && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
bio-spatial-transcriptomics-spatial-proteomics
GitHub stars
3.1k
Used in
1 other repo
Token cost
~976 tokens
SKILL.md length
179 words
Files
3
Skills in repo
173
Repo updated
First seen
Licence
None found

At a glance

Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization.

  • Working with multiplexed imaging data
  • SKILL.md covers Version Compatibility, Data Loading, Preprocessing and Phenotyping Cells, plus 5 more sections
  • Runs Python scripts from its folder; calls pip
  • Analyzing protein spatial patterns

What it does

Bio Spatial Transcriptomics Spatial Proteomics is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization. Use when working with multiplexed imaging data, analyzing protein spatial patterns, or integrating spatial proteomics with transcriptomics.

Its SKILL.md is about 980 tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/spatial_proteomics_analysis.py` and `usage-guide.md`).

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.

When your agent uses it

  • Working with multiplexed imaging data
  • Analyzing protein spatial patterns
  • Integrating spatial proteomics with transcriptomics

Example prompts

  • “Use the bio-spatial-transcriptomics-spatial-proteomics skill to analyz spatial proteomics data from CODEX, IMC, and MIBI platforms including cell…”
  • “/bio-spatial-transcriptomics-spatial-proteomics”

Requirements

  • Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit b1f9b6e. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships script files (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • pip

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Bio Spatial Transcriptomics Spatial Proteomics loads about 976 tokens when it runs. Until then it costs about 78 tokens; SKILL.md has 179 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~78
When it runs · the whole SKILL.md, loaded when a task matches
~976

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

Without a licence we can't republish the file, so here is its outline and opening line. It has 179 words (~976 tokens).

“Reference examples tested with: anndata 0.10+, scanpy 1.10+, squidpy 1.3+”

— opening of SKILL.md by FreedomIntelligence
name
bio-spatial-transcriptomics-spatial-proteomics
tool_type
python
primary_tool
scimap

Read the full SKILL.md on GitHub

Files

SKILL.md and 2 other files in skills/bio-spatial-transcriptomics-spatial-proteomics of FreedomIntelligence/OpenClaw-Medical-Skills.

  • SKILL.md
  • examples/spatial_proteomics_analysis.py
  • usage-guide.md

Open the folder on GitHubat commit b1f9b6e

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Bio Spatial Transcriptomics Spatial Proteomics next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Bio Spatial Transcriptomics Spatial Proteomics compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bio Spatial Transcriptomics Spatial Proteomics this skillFreedomIntelligence/OpenClaw-Medical-Skills3.1k1 repos~976Automated safety check: PassNone
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Clinvar Databasegoogle-deepmind/science-skills3.2k2 repos~3.9kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
Dbsnp Databasegoogle-deepmind/science-skills3.2k2 repos~3.4kAutomated safety check: NotesApache-2.0

Similar skills

  • Alphagenome Single Variant Analysis

    google-deepmind/science-skills

    Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.

    3.2k GitHub starsUsed in 2 repos~3k tokens
    Research & ScienceAuto-check: notes

  • 13C Metabolic Flux Analysis

    K-Dense-AI/scientific-agent-skills

    Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.

    48k GitHub starsUsed in 1 repo~3.2k tokens
    Research & ScienceAuto-check passed

  • Clinvar Database

    google-deepmind/science-skills

    A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…

    3.2k GitHub starsUsed in 2 repos~3.9k tokens
    Research & ScienceAuto-check: notes

  • Metabolic Study Planner

    aiming-lab/AutoResearchClaw

    Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.

    15k GitHub stars~1.9k tokensUpdated 1 mo ago
    Research & ScienceAuto-check passed

  • Dbsnp Database

    google-deepmind/science-skills

    A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.

    3.2k GitHub starsUsed in 2 repos~3.4k tokens
    Research & ScienceAuto-check: notes

  • MFA Pipeline Orchestrator

    aiming-lab/AutoResearchClaw

    Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.

    15k GitHub stars~923 tokensUpdated 1 mo ago
    Research & ScienceAuto-check passed

More from FreedomIntelligence/OpenClaw-Medical-Skills

All 173 skills in this repo

  • Differentiation Schemes

    FreedomIntelligence/OpenClaw-Medical-Skills

    Select and apply numerical differentiation schemes for PDE/ODE discretization.

    3.1k GitHub starsUsed in 1 repo~1.4k tokens
    Auto-check: notes

  • Medical Research Toolkit

    FreedomIntelligence/OpenClaw-Medical-Skills

    Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research.

    3.1k GitHub starsUsed in 1 repo~2.4k tokens
    Auto-check passed

  • Mesh Generation

    FreedomIntelligence/OpenClaw-Medical-Skills

    Plan and evaluate mesh generation for numerical simulations.

    3.1k GitHub starsUsed in 1 repo~1.1k tokens
    Auto-check: notes

  • Numerical Integration

    FreedomIntelligence/OpenClaw-Medical-Skills

    Select and configure time integration methods for ODE/PDE simulations.

    3.1k GitHub starsUsed in 1 repo~1.5k tokens
    Auto-check: notes

  • Ontology Explorer

    FreedomIntelligence/OpenClaw-Medical-Skills

    Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy).

    3.1k GitHub starsUsed in 1 repo~2k tokens
    Auto-check: notes

  • Ontology Mapper

    FreedomIntelligence/OpenClaw-Medical-Skills

    Map materials science terms, crystal structures, and sample descriptions to ontology classes and properties.

    3.1k GitHub starsUsed in 1 repo~1.9k tokens
    Auto-check: notes

Categories

Questions about Bio Spatial Transcriptomics Spatial Proteomics

What does Bio Spatial Transcriptomics Spatial Proteomics do?

Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization. Bio Spatial Transcriptomics Spatial Proteomics is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization.

When should I use Bio Spatial Transcriptomics Spatial Proteomics?

Bio Spatial Transcriptomics Spatial Proteomics fits situations like: working with multiplexed imaging data; analyzing protein spatial patterns; integrating spatial proteomics with transcriptomics.

How do I install Bio Spatial Transcriptomics Spatial Proteomics in Claude Code?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-proteomics -a claude-code`. Or copy the skill folder (skills/bio-spatial-transcriptomics-spatial-proteomics in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-spatial-transcriptomics-spatial-proteomics in your project. Claude Code loads it when a task matches its description.

How do I install Bio Spatial Transcriptomics Spatial Proteomics in Codex?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-proteomics -a codex`. Or copy the skill folder (skills/bio-spatial-transcriptomics-spatial-proteomics in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-spatial-transcriptomics-spatial-proteomics in your project. Codex loads it when a task matches its description.

Can I use Bio Spatial Transcriptomics Spatial Proteomics in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-proteomics -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-spatial-transcriptomics-spatial-proteomics, .gemini/skills/bio-spatial-transcriptomics-spatial-proteomics, .github/skills/bio-spatial-transcriptomics-spatial-proteomics and .opencode/skills/bio-spatial-transcriptomics-spatial-proteomics in your project.

What does Bio Spatial Transcriptomics Spatial Proteomics need to run?

Going by SKILL.md and its folder, Bio Spatial Transcriptomics Spatial Proteomics needs Python for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3.

Does Bio Spatial Transcriptomics Spatial Proteomics access the network?

SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.

Is Bio Spatial Transcriptomics Spatial Proteomics safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Bio Spatial Transcriptomics Spatial Proteomics use?

No licence was found for Bio Spatial Transcriptomics Spatial Proteomics or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Bio Spatial Transcriptomics Spatial Proteomics use?

About 976 tokens (SKILL.md is roughly 3.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Bio Spatial Transcriptomics Spatial Proteomics?

Skills that share tags, products or a category with Bio Spatial Transcriptomics Spatial Proteomics: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bio Spatial Transcriptomics Spatial Proteomics?

FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,051 GitHub stars. The repository holds 173 skills in this directory. The repository was last updated on July 21, 2026.

Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.