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Agent skill

Bio Spatial Transcriptomics Spatial Domains

by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills

Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy.

No licenceAuto-check passedResearch & Science

Install Bio Spatial Transcriptomics Spatial Domains

skills CLI
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-domains -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-domains --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-domains .claude/skills/bio-spatial-transcriptomics-spatial-domains && 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-domains
GitHub stars
3.1k
Used in
1 other repo
Token cost
~2.1k tokens
SKILL.md length
380 words
Files
3
Skills in repo
279
Repo updated
First seen
Licence
None found

At a glance

Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy.

  • Identifying tissue domains
  • SKILL.md covers Version Compatibility, Required Imports, Standard Clustering… and Spatial-Aware Clustering with…, plus 9 more sections
  • Runs Python scripts from its folder; calls pip
  • Spatial regions

What it does

Bio Spatial Transcriptomics Spatial Domains is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy. Cluster spots considering both expression and spatial context to define anatomical regions. Use when identifying tissue domains or spatial regions.

Its SKILL.md is about 2.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/detect_domains.py` and `usage-guide.md`).

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

When your agent uses it

  • Identifying tissue domains
  • Spatial regions

Example prompts

  • “/bio-spatial-transcriptomics-spatial-domains”

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 Domains loads about 2.1k tokens when it runs. Until then it costs about 73 tokens; SKILL.md has 380 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~73
When it runs · the whole SKILL.md, loaded when a task matches
~2.1k

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 380 words (~2,117 tokens).

“Reference examples tested with: matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scikit-learn 1.4+, scipy 1.12+, squidpy 1.3+”

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

Read the full SKILL.md on GitHub

Files

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

  • SKILL.md
  • examples/detect_domains.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 9, 2026.

Compare with similar skills

Bio Spatial Transcriptomics Spatial Domains 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 Domains compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bio Spatial Transcriptomics Spatial Domains this skillFreedomIntelligence/OpenClaw-Medical-Skills3.1k1 repos~2.1kAutomated safety check: PassNone
Scanpy Single-Cell Analysisdavila7/claude-code-templates32k15 repos~2.8kAutomated safety check: PassMIT
Single Cell Rna AnalysisPKU-YuanGroup/OpenAI4S620—~1.3kAutomated safety check: PassMIT
Anndatadavila7/claude-code-templates32k11 repos~2.5kAutomated safety check: PassMIT
Cellxgene Censusdavila7/claude-code-templates32k11 repos~3.8kAutomated safety check: PassMIT
Bulk RnaseqK-Dense-AI/scientific-agent-skills48k1 repos~4.2kAutomated safety check: PassMIT

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Works with

Categories

Questions about Bio Spatial Transcriptomics Spatial Domains

What does Bio Spatial Transcriptomics Spatial Domains do?

Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy. Bio Spatial Transcriptomics Spatial Domains is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy.

When should I use Bio Spatial Transcriptomics Spatial Domains?

Bio Spatial Transcriptomics Spatial Domains fits situations like: identifying tissue domains; spatial regions.

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

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

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

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

Can I use Bio Spatial Transcriptomics Spatial Domains 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-domains -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-domains, .gemini/skills/bio-spatial-transcriptomics-spatial-domains, .github/skills/bio-spatial-transcriptomics-spatial-domains and .opencode/skills/bio-spatial-transcriptomics-spatial-domains in your project.

What does Bio Spatial Transcriptomics Spatial Domains need to run?

Going by SKILL.md and its folder, Bio Spatial Transcriptomics Spatial Domains 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 Domains 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 Domains 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 Domains use?

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

How many tokens does Bio Spatial Transcriptomics Spatial Domains use?

About 2.1k tokens (SKILL.md is roughly 8.5k 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 Domains?

Skills that share tags, products or a category with Bio Spatial Transcriptomics Spatial Domains: Scanpy Single-Cell Analysis (davila7/claude-code-templates, 32k stars), Single Cell Rna Analysis (PKU-YuanGroup/OpenAI4S, 620 stars), Anndata (davila7/claude-code-templates, 32k stars) and Cellxgene Census (davila7/claude-code-templates, 32k 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 Domains?

FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 GitHub stars. The repository holds 279 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.