Scanpy Single-Cell Analysis
davila7/claude-code-templates
Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.
Agent skill
Bio Imaging Mass Cytometry Phenotyping
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Cell type assignment from marker expression in IMC data. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.
Install Bio Imaging Mass Cytometry Phenotyping
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-imaging-mass-cytometry-phenotyping -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-imaging-mass-cytometry-phenotyping --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-imaging-mass-cytometry-phenotyping .claude/skills/bio-imaging-mass-cytometry-phenotyping && rm -rf skills-srcUse ~/.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/
Install the "bio-imaging-mass-cytometry-phenotyping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-imaging-mass-cytometry-phenotyping into .claude/skills/bio-imaging-mass-cytometry-phenotyping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-imaging-mass-cytometry-phenotyping", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-imaging-mass-cytometry-phenotypingType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-imaging-mass-cytometry-phenotyping -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-imaging-mass-cytometry-phenotyping --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bio-imaging-mass-cytometry-phenotyping .agents/skills/bio-imaging-mass-cytometry-phenotyping && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-imaging-mass-cytometry-phenotyping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-imaging-mass-cytometry-phenotyping into .agents/skills/bio-imaging-mass-cytometry-phenotyping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-imaging-mass-cytometry-phenotyping", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-imaging-mass-cytometry-phenotyping -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-imaging-mass-cytometry-phenotyping --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bio-imaging-mass-cytometry-phenotyping .cursor/skills/bio-imaging-mass-cytometry-phenotyping && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "bio-imaging-mass-cytometry-phenotyping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-imaging-mass-cytometry-phenotyping into .cursor/skills/bio-imaging-mass-cytometry-phenotyping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-imaging-mass-cytometry-phenotyping", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/bio-imaging-mass-cytometry-phenotyping--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-imaging-mass-cytometry-phenotyping -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-imaging-mass-cytometry-phenotyping --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bio-imaging-mass-cytometry-phenotyping .gemini/skills/bio-imaging-mass-cytometry-phenotyping && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "bio-imaging-mass-cytometry-phenotyping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-imaging-mass-cytometry-phenotyping into .gemini/skills/bio-imaging-mass-cytometry-phenotyping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-imaging-mass-cytometry-phenotyping", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-imaging-mass-cytometry-phenotypingInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-imaging-mass-cytometry-phenotyping -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bio-imaging-mass-cytometry-phenotyping .github/skills/bio-imaging-mass-cytometry-phenotyping && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "bio-imaging-mass-cytometry-phenotyping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-imaging-mass-cytometry-phenotyping into .github/skills/bio-imaging-mass-cytometry-phenotyping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-imaging-mass-cytometry-phenotyping", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-imaging-mass-cytometry-phenotyping -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-imaging-mass-cytometry-phenotyping --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bio-imaging-mass-cytometry-phenotyping .opencode/skills/bio-imaging-mass-cytometry-phenotyping && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "bio-imaging-mass-cytometry-phenotyping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-imaging-mass-cytometry-phenotyping into .opencode/skills/bio-imaging-mass-cytometry-phenotyping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-imaging-mass-cytometry-phenotyping", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
bio-imaging-mass-cytometry-phenotyping- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~1.7k tokens
- SKILL.md length
- 196 words
- Files
- 3
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Cell type assignment from marker expression in IMC data. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.
- Assigning cell types to segmented IMC cells based on protein marker expression
- SKILL.md covers Version Compatibility, Load Single-Cell Data, Data Transformation and Clustering-Based Phenotyping, plus 8 more sections
- Runs Python scripts from its folder; calls pip
- Phenotyping cells in multiplexed imaging data
What it does
Bio Imaging Mass Cytometry Phenotyping is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Cell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assigning cell types to segmented IMC cells based on protein marker expression or when phenotyping cells in multiplexed imaging data.
Its SKILL.md is about 1.7k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/phenotype_cells.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
- Assigning cell types to segmented IMC cells based on protein marker expression
- Phenotyping cells in multiplexed imaging data
Example prompts
- “/bio-imaging-mass-cytometry-phenotyping”
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 Imaging Mass Cytometry Phenotyping loads about 1.7k tokens when it runs. Until then it costs about 78 tokens; SKILL.md has 196 words of instructions outside code blocks.
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 196 words (~1,726 tokens).
“Reference examples tested with: FlowSOM 2.10+, anndata 0.10+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scikit-learn 1.4+”
- name
- bio-imaging-mass-cytometry-phenotyping
- tool_type
- python
- primary_tool
- scanpy
Files
SKILL.md and 2 other files in skills/bio-imaging-mass-cytometry-phenotyping of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/phenotype_cells.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 Imaging Mass Cytometry Phenotyping 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Bio Imaging Mass Cytometry Phenotyping this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.7k | Automated safety check: Pass | None | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 33k | 15 repos | ~2.8k | Automated safety check: Pass | MIT | |
| Bulkrna Cosinor RhythmTianGzlab/OmicsClaw | 161 | — | ~840 | Automated safety check: Pass | Apache-2.0 | |
| deepTools NGS Toolkitdavila7/claude-code-templates | 33k | 12 repos | ~4.5k | Automated safety check: Pass | MIT | |
| LaminDB Biological Data Managementdavila7/claude-code-templates | 33k | 12 repos | ~3.6k | Automated safety check: Pass | MIT | |
| PyDESeq2 Differential Expressiondavila7/claude-code-templates | 33k | 11 repos | ~4k | Automated safety check: Pass | MIT |
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Related
Categories
Questions about Bio Imaging Mass Cytometry Phenotyping
What does Bio Imaging Mass Cytometry Phenotyping do?
Cell type assignment from marker expression in IMC data. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Bio Imaging Mass Cytometry Phenotyping is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Cell type assignment from marker expression in IMC data.
When should I use Bio Imaging Mass Cytometry Phenotyping?
Bio Imaging Mass Cytometry Phenotyping fits situations like: assigning cell types to segmented IMC cells based on protein marker expression; phenotyping cells in multiplexed imaging data.
How do I install Bio Imaging Mass Cytometry Phenotyping in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-imaging-mass-cytometry-phenotyping -a claude-code`. Or copy the skill folder (skills/bio-imaging-mass-cytometry-phenotyping in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-imaging-mass-cytometry-phenotyping in your project. Claude Code loads it when a task matches its description.
How do I install Bio Imaging Mass Cytometry Phenotyping in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-imaging-mass-cytometry-phenotyping -a codex`. Or copy the skill folder (skills/bio-imaging-mass-cytometry-phenotyping in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-imaging-mass-cytometry-phenotyping in your project. Codex loads it when a task matches its description.
Can I use Bio Imaging Mass Cytometry Phenotyping 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-imaging-mass-cytometry-phenotyping -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-imaging-mass-cytometry-phenotyping, .gemini/skills/bio-imaging-mass-cytometry-phenotyping, .github/skills/bio-imaging-mass-cytometry-phenotyping and .opencode/skills/bio-imaging-mass-cytometry-phenotyping in your project.
What does Bio Imaging Mass Cytometry Phenotyping need to run?
Going by SKILL.md and its folder, Bio Imaging Mass Cytometry Phenotyping needs Python for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3.
Does Bio Imaging Mass Cytometry Phenotyping 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 Imaging Mass Cytometry Phenotyping 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 Imaging Mass Cytometry Phenotyping use?
No licence was found for Bio Imaging Mass Cytometry Phenotyping or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Imaging Mass Cytometry Phenotyping use?
About 1.7k tokens (SKILL.md is roughly 6.9k 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 Imaging Mass Cytometry Phenotyping?
Skills that share tags, products or a category with Bio Imaging Mass Cytometry Phenotyping: Scanpy Single-Cell Analysis (davila7/claude-code-templates, 33k stars), Bulkrna Cosinor Rhythm (TianGzlab/OmicsClaw, 161 stars), deepTools NGS Toolkit (davila7/claude-code-templates, 33k stars) and LaminDB Biological Data Management (davila7/claude-code-templates, 33k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Imaging Mass Cytometry Phenotyping?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,053 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.