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Agent skill

Bio Spatial Transcriptomics Spatial Multiomics

by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills

Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD.

No licenceAuto-check passedResearch & Science

Install Bio Spatial Transcriptomics Spatial Multiomics

skills CLI
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-multiomics -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-multiomics --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-multiomics .claude/skills/bio-spatial-transcriptomics-spatial-multiomics && 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-multiomics
GitHub stars
3.1k
Used in
1 other repo
Token cost
~1.6k tokens
SKILL.md length
282 words
Files
4
Skills in repo
173
Repo updated
First seen
Licence
None found

At a glance

Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD.

  • Working with subcellular resolution
  • SKILL.md covers Version Compatibility, Platform Comparison, Squidpy for High-Resolution Data and SpatialData Framework, plus 6 more sections
  • Runs Python scripts from its folder; calls pip
  • High-density spatial data

What it does

Bio Spatial Transcriptomics Spatial Multiomics is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.

Its SKILL.md is about 1.6k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `examples/spatialdata_workflow.py`, `examples/squidpy_highres.py` and `usage-guide.md`).

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

When your agent uses it

  • Working with subcellular resolution
  • High-density spatial data

Example prompts

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

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 Multiomics loads about 1.6k tokens when it runs. Until then it costs about 52 tokens; SKILL.md has 282 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~52
When it runs · the whole SKILL.md, loaded when a task matches
~1.6k

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 282 words (~1,577 tokens).

“Reference examples tested with: Cellpose 3.0+, matplotlib 3.8+, numpy 1.26+, scanpy 1.10+, scipy 1.12+, spatialdata 0.1+, squidpy 1.3+”

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

Read the full SKILL.md on GitHub

Files

SKILL.md and 3 other files in skills/bio-spatial-transcriptomics-spatial-multiomics of FreedomIntelligence/OpenClaw-Medical-Skills.

  • SKILL.md
  • examples/spatialdata_workflow.py
  • examples/squidpy_highres.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 Multiomics 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 Multiomics compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bio Spatial Transcriptomics Spatial Multiomics this skillFreedomIntelligence/OpenClaw-Medical-Skills3.1k1 repos~1.6kAutomated safety check: PassNone
Single2spatial Spatial Mappingmajiayu000/claude-skill-registry6663 repos~994Automated safety check: PassMIT
Bioconductor SpotcleanbioMate-AI/biomate-bioconductor-kb804—~1.5kAutomated safety check: PassCustom licence
Pathmldavila7/claude-code-templates32k12 repos~1.9kAutomated safety check: PassMIT
Deepspot MK-Dense-AI/scientific-agent-skills48k1 repos~2.5kAutomated safety check: NotesPolyForm-Noncommercial-1.0.0
Bio Spatial Transcriptomics High Resolution BinningGPTomics/bioSkills1.2k1 repos~3.7kAutomated safety check: PassMIT

Similar skills

  • Single2spatial Spatial Mapping

    majiayu000/claude-skill-registry

    Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.

    666 GitHub starsUsed in 3 repos~994 tokens
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  • Bioconductor Spotclean

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    SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data.

    804 GitHub stars~1.5k tokensUpdated 3 mo ago
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  • Pathml

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    48k GitHub starsUsed in 1 repo~2.5k tokens
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  • Bio Spatial Transcriptomics High Resolution Binning

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Categories

Questions about Bio Spatial Transcriptomics Spatial Multiomics

What does Bio Spatial Transcriptomics Spatial Multiomics do?

Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Bio Spatial Transcriptomics Spatial Multiomics is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD.

When should I use Bio Spatial Transcriptomics Spatial Multiomics?

Bio Spatial Transcriptomics Spatial Multiomics fits situations like: working with subcellular resolution; high-density spatial data.

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

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

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

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

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

What does Bio Spatial Transcriptomics Spatial Multiomics need to run?

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

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

How many tokens does Bio Spatial Transcriptomics Spatial Multiomics use?

About 1.6k tokens (SKILL.md is roughly 6.3k 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 Multiomics?

Skills that share tags, products or a category with Bio Spatial Transcriptomics Spatial Multiomics: Single2spatial Spatial Mapping (majiayu000/claude-skill-registry, 666 stars), Bioconductor Spotclean (bioMate-AI/biomate-bioconductor-kb, 804 stars), Pathml (davila7/claude-code-templates, 32k stars) and Deepspot M (K-Dense-AI/scientific-agent-skills, 48k 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 Multiomics?

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.