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Agent skill

Bio Spatial Transcriptomics Image Analysis

by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills

Process and analyze tissue images from spatial transcriptomics data using Squidpy.

No licenceAuto-check passedResearch & Science

Install Bio Spatial Transcriptomics Image Analysis

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

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

GitHub CLI
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-spatial-transcriptomics-image-analysis --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-image-analysis .claude/skills/bio-spatial-transcriptomics-image-analysis && 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-image-analysis
GitHub stars
3.1k
Used in
1 other repo
Token cost
~2k tokens
SKILL.md length
333 words
Files
3
Skills in repo
170
Repo updated
First seen
Licence
None found

At a glance

Process and analyze tissue images from spatial transcriptomics data using Squidpy.

  • Processing tissue images for spatial transcriptomics
  • SKILL.md covers Version Compatibility, Required Imports, Access Tissue Images and Create ImageContainer, plus 10 more sections
  • Runs Python scripts from its folder; calls pip
  • Tasks that involve Bioinformatics

What it does

Bio Spatial Transcriptomics Image Analysis is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei, and compute morphological features from H&E or IF images. Use when processing tissue images for spatial transcriptomics.

Its SKILL.md is about 2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/extract_features.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

  • Processing tissue images for spatial transcriptomics
  • Tasks that involve Bioinformatics

Example prompts

  • “/bio-spatial-transcriptomics-image-analysis”

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 Image Analysis loads about 2k tokens when it runs. Until then it costs about 73 tokens; SKILL.md has 333 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
~2k

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 333 words (~1,996 tokens).

“Reference examples tested with: Cellpose 3.0+, 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-image-analysis
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-image-analysis of FreedomIntelligence/OpenClaw-Medical-Skills.

  • SKILL.md
  • examples/extract_features.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 Image Analysis 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 Image Analysis compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bio Spatial Transcriptomics Image Analysis this skillFreedomIntelligence/OpenClaw-Medical-Skills3.1k1 repos~2kAutomated safety check: PassNone
Dbsnp Databasegoogle-deepmind/science-skills3.2k3 repos~3.4kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
MFA Pipeline Orchestratoraiming-lab/AutoResearchClaw15k—~923Automated safety check: PassMIT

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Categories

Questions about Bio Spatial Transcriptomics Image Analysis

What does Bio Spatial Transcriptomics Image Analysis do?

Process and analyze tissue images from spatial transcriptomics data using Squidpy. Bio Spatial Transcriptomics Image Analysis is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Process and analyze tissue images from spatial transcriptomics data using Squidpy.

When should I use Bio Spatial Transcriptomics Image Analysis?

Bio Spatial Transcriptomics Image Analysis fits situations like: processing tissue images for spatial transcriptomics; tasks that involve Bioinformatics.

How do I install Bio Spatial Transcriptomics Image Analysis in Claude Code?

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

How do I install Bio Spatial Transcriptomics Image Analysis in Codex?

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

Can I use Bio Spatial Transcriptomics Image Analysis 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-image-analysis -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-image-analysis, .gemini/skills/bio-spatial-transcriptomics-image-analysis, .github/skills/bio-spatial-transcriptomics-image-analysis and .opencode/skills/bio-spatial-transcriptomics-image-analysis in your project.

What does Bio Spatial Transcriptomics Image Analysis need to run?

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

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

How many tokens does Bio Spatial Transcriptomics Image Analysis use?

About 2k tokens (SKILL.md is roughly 8k 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 Image Analysis?

Skills that share tags, products or a category with Bio Spatial Transcriptomics Image Analysis: Dbsnp Database (google-deepmind/science-skills, 3.2k stars), Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars) and Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k 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 Image Analysis?

FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 GitHub stars. The repository holds 170 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.