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Agent skill

Bio Spatial Transcriptomics Spatial Data Io

by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills

Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData.

No licenceAuto-check passedResearch & Science

Install Bio Spatial Transcriptomics Spatial Data Io

skills CLI
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-data-io -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-data-io --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-data-io .claude/skills/bio-spatial-transcriptomics-spatial-data-io && 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-data-io
GitHub stars
3.1k
Used in
1 other repo
Token cost
~2k tokens
SKILL.md length
409 words
Files
3
Skills in repo
173
Repo updated
First seen
Licence
None found

At a glance

Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData.

  • Other spatial data
  • SKILL.md covers Version Compatibility, Required Imports, Load 10X Visium Data and Load Visium with Scanpy, plus 14 more sections
  • Runs Python scripts from its folder; calls pip
  • Tasks that involve Bioinformatics

What it does

Bio Spatial Transcriptomics Spatial Data Io is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. Read Space Ranger outputs, convert formats, and access spatial coordinates. Use when loading Visium, Xenium, MERFISH, or other spatial data.

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/load_visium.py` and `usage-guide.md`).

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

When your agent uses it

  • Other spatial data
  • Tasks that involve Bioinformatics
  • Tasks that involve Slides and decks

Example prompts

  • “/bio-spatial-transcriptomics-spatial-data-io”

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 Data Io loads about 2k tokens when it runs. Until then it costs about 78 tokens; SKILL.md has 409 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
~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 409 words (~2,022 tokens).

“Reference examples tested with: anndata 0.10+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, spatialdata 0.1+, squidpy 1.3+”

— opening of SKILL.md by FreedomIntelligence
name
bio-spatial-transcriptomics-spatial-data-io
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-data-io of FreedomIntelligence/OpenClaw-Medical-Skills.

  • SKILL.md
  • examples/load_visium.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 Data Io 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 Data Io compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bio Spatial Transcriptomics Spatial Data Io this skillFreedomIntelligence/OpenClaw-Medical-Skills3.1k1 repos~2kAutomated safety check: PassNone
Scanpy Single-Cell Analysisdavila7/claude-code-templates32k16 repos~2.8kAutomated safety check: PassMIT
Anndatadavila7/claude-code-templates32k12 repos~2.5kAutomated safety check: PassMIT
ScanpyK-Dense-AI/scientific-agent-skills48k1 repos~5.1kAutomated safety check: PassBSD-3-Clause
Cellxgene CensusK-Dense-AI/scientific-agent-skills48k1 repos~3.4kAutomated safety check: NotesMIT
Omics ToolsDrugClaw/DrugClaw125—~1.1kAutomated safety check: PassApache-2.0

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Works with

Categories

Questions about Bio Spatial Transcriptomics Spatial Data Io

What does Bio Spatial Transcriptomics Spatial Data Io do?

Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. Bio Spatial Transcriptomics Spatial Data Io is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData.

When should I use Bio Spatial Transcriptomics Spatial Data Io?

Bio Spatial Transcriptomics Spatial Data Io fits situations like: other spatial data; tasks that involve Bioinformatics; tasks that involve Slides and decks.

How do I install Bio Spatial Transcriptomics Spatial Data Io in Claude Code?

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

How do I install Bio Spatial Transcriptomics Spatial Data Io in Codex?

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

Can I use Bio Spatial Transcriptomics Spatial Data Io 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-data-io -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-data-io, .gemini/skills/bio-spatial-transcriptomics-spatial-data-io, .github/skills/bio-spatial-transcriptomics-spatial-data-io and .opencode/skills/bio-spatial-transcriptomics-spatial-data-io in your project.

What does Bio Spatial Transcriptomics Spatial Data Io need to run?

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

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

How many tokens does Bio Spatial Transcriptomics Spatial Data Io use?

About 2k tokens (SKILL.md is roughly 8.1k 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 Data Io?

Skills that share tags, products or a category with Bio Spatial Transcriptomics Spatial Data Io: Scanpy Single-Cell Analysis (davila7/claude-code-templates, 32k stars), Anndata (davila7/claude-code-templates, 32k stars), Scanpy (K-Dense-AI/scientific-agent-skills, 48k stars) and Cellxgene Census (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 Data Io?

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.