Deepspot M
K-Dense-AI/scientific-agent-skills
Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M.
Agent skill
Spatial Transcriptomics Tutorials With Omicverse
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq…
Install Spatial Transcriptomics Tutorials With Omicverse
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill spatial-transcriptomics-tutorials-with-omicverse -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills spatial-transcriptomics-tutorials-with-omicverse --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/spatial-tutorials .claude/skills/spatial-transcriptomics-tutorials-with-omicverse && 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 "spatial-transcriptomics-tutorials-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/spatial-tutorials into .claude/skills/spatial-transcriptomics-tutorials-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-transcriptomics-tutorials-with-omicverse", 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/spatial-tutorialsType 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 spatial-transcriptomics-tutorials-with-omicverse -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills spatial-transcriptomics-tutorials-with-omicverse --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/spatial-tutorials .agents/skills/spatial-transcriptomics-tutorials-with-omicverse && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "spatial-transcriptomics-tutorials-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/spatial-tutorials into .agents/skills/spatial-transcriptomics-tutorials-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-transcriptomics-tutorials-with-omicverse", 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 spatial-transcriptomics-tutorials-with-omicverse -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills spatial-transcriptomics-tutorials-with-omicverse --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/spatial-tutorials .cursor/skills/spatial-transcriptomics-tutorials-with-omicverse && 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 "spatial-transcriptomics-tutorials-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/spatial-tutorials into .cursor/skills/spatial-transcriptomics-tutorials-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-transcriptomics-tutorials-with-omicverse", 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/spatial-tutorials--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 spatial-transcriptomics-tutorials-with-omicverse -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills spatial-transcriptomics-tutorials-with-omicverse --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/spatial-tutorials .gemini/skills/spatial-transcriptomics-tutorials-with-omicverse && 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 "spatial-transcriptomics-tutorials-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/spatial-tutorials into .gemini/skills/spatial-transcriptomics-tutorials-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-transcriptomics-tutorials-with-omicverse", 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 spatial-transcriptomics-tutorials-with-omicverseInstalls 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 spatial-transcriptomics-tutorials-with-omicverse -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/spatial-tutorials .github/skills/spatial-transcriptomics-tutorials-with-omicverse && 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 "spatial-transcriptomics-tutorials-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/spatial-tutorials into .github/skills/spatial-transcriptomics-tutorials-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-transcriptomics-tutorials-with-omicverse", 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 spatial-transcriptomics-tutorials-with-omicverse -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 spatial-transcriptomics-tutorials-with-omicverse --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/spatial-tutorials .opencode/skills/spatial-transcriptomics-tutorials-with-omicverse && 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 "spatial-transcriptomics-tutorials-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/spatial-tutorials into .opencode/skills/spatial-transcriptomics-tutorials-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-transcriptomics-tutorials-with-omicverse", 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
spatial-transcriptomics-tutorials-with-omicverse- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~3.7k tokens
- SKILL.md length
- 950 words
- Files
- 2
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq…
- Works in 3 steps: Load spatial slides and manipulate… → Segment Visium HD tiles into cells → Initial QC for downstream tasks
- Tasks that involve Bioinformatics
- SKILL.md covers Overview, Instructions, Dependencies and Critical functions and…, plus 3 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Spatial Transcriptomics Tutorials With Omicverse is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq datasets.
Its SKILL.md is about 3.7k tokens, which your agent loads only when the skill is triggered. The skill folder holds 1 other file (for example `reference.md`).
It sits in Research & Science, covering Bioinformatics and Slides and decks. It works with Jupyter. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Tasks that involve Bioinformatics
- Tasks that involve Slides and decks
Example prompts
- “/spatial-transcriptomics-tutorials-with-omicverse”
Requirements
- Python 3
Workflow steps
3 steps, taken from the first numbered list in SKILL.md.
- Load spatial slides and manipulate coordinates
- Segment Visium HD tiles into cells
- Initial QC for downstream tasks
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
No scripts in the folder and no shell commands in SKILL.md.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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
Spatial Transcriptomics Tutorials With Omicverse loads about 3.7k tokens when it runs. Until then it costs about 63 tokens; SKILL.md has 950 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 950 words (~3,670 tokens).
“Use this skill to navigate the spatial analysis tutorials located under Tutorials-space. The notebooks span preprocessing utilities (t_crop_rotate.ipynb, t_cellpose.ipynb), deconvolution frameworks (t_decov.ipynb, t_starfysh.ipynb), and downstream spatial modelling or integration tasks (t_cluster_space.ipynb, t_staligner.ipynb, t_spaceflow.ipynb, t_commot_flowsig.ipynb, t_gaston.ipynb, t_slat.ipynb, t_stt.ipynb). Follow the staged…”
- name
- spatial-transcriptomics-tutorials-with-omicverse
- title
- Spatial transcriptomics tutorials with omicverse
Files
SKILL.md and 1 other file in skills/spatial-tutorials of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- reference.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
Spatial Transcriptomics Tutorials With Omicverse 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 |
|---|---|---|---|---|---|---|
| Spatial Transcriptomics Tutorials With Omicverse this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~3.7k | Automated safety check: Pass | None | |
| Deepspot MK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~2.5k | Automated safety check: Notes | PolyForm-Noncommercial-1.0.0 | |
| Pixi Environment Builderxuzhougeng/wisp-science | 1k | — | ~3.7k | Automated safety check: Pass | AGPL-3.0 | |
| Bio Spatial Transcriptomics High Resolution BinningGPTomics/bioSkills | 1.2k | 1 repos | ~3.7k | Automated safety check: Pass | MIT | |
| Bio Spatial Transcriptomics Spatial DomainsGPTomics/bioSkills | 1.2k | 1 repos | ~4.8k | Automated safety check: Pass | MIT | |
| Bioconductor NnsvgbioMate-AI/biomate-bioconductor-kb | 804 | — | ~925 | Automated safety check: Pass | Custom licence |
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Related
Works with
Categories
Questions about Spatial Transcriptomics Tutorials With Omicverse
What does Spatial Transcriptomics Tutorials With Omicverse do?
Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq…. Spatial Transcriptomics Tutorials With Omicverse is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq datasets.
When should I use Spatial Transcriptomics Tutorials With Omicverse?
Spatial Transcriptomics Tutorials With Omicverse fits situations like: tasks that involve Bioinformatics; tasks that involve Slides and decks.
How do I install Spatial Transcriptomics Tutorials With Omicverse in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill spatial-transcriptomics-tutorials-with-omicverse -a claude-code`. Or copy the skill folder (skills/spatial-tutorials in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/spatial-transcriptomics-tutorials-with-omicverse in your project. Claude Code loads it when a task matches its description.
How do I install Spatial Transcriptomics Tutorials With Omicverse in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill spatial-transcriptomics-tutorials-with-omicverse -a codex`. Or copy the skill folder (skills/spatial-tutorials in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/spatial-transcriptomics-tutorials-with-omicverse in your project. Codex loads it when a task matches its description.
Can I use Spatial Transcriptomics Tutorials With Omicverse 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 spatial-transcriptomics-tutorials-with-omicverse -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/spatial-transcriptomics-tutorials-with-omicverse, .gemini/skills/spatial-transcriptomics-tutorials-with-omicverse, .github/skills/spatial-transcriptomics-tutorials-with-omicverse and .opencode/skills/spatial-transcriptomics-tutorials-with-omicverse in your project.
What does Spatial Transcriptomics Tutorials With Omicverse need to run?
SKILL.md names no scripts, command-line tools or credentials: Spatial Transcriptomics Tutorials With Omicverse is instructions for the agent only. Our summary lists: Python 3.
Does Spatial Transcriptomics Tutorials With Omicverse access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Spatial Transcriptomics Tutorials With Omicverse 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 Spatial Transcriptomics Tutorials With Omicverse use?
No licence was found for Spatial Transcriptomics Tutorials With Omicverse or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Spatial Transcriptomics Tutorials With Omicverse use?
About 3.7k tokens (SKILL.md is roughly 15k 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 Spatial Transcriptomics Tutorials With Omicverse?
Skills that share tags, products or a category with Spatial Transcriptomics Tutorials With Omicverse: Deepspot M (K-Dense-AI/scientific-agent-skills, 48k stars), Pixi Environment Builder (xuzhougeng/wisp-science, 1k stars), Bio Spatial Transcriptomics High Resolution Binning (GPTomics/bioSkills, 1.2k stars) and Bio Spatial Transcriptomics Spatial Domains (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Spatial Transcriptomics Tutorials With Omicverse?
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.