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Agent skill

Deepspot M

by K-Dense-AI in K-Dense-AI/scientific-agent-skills

Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M.

PolyForm-Noncommercial-1.0.0Auto-check: notesResearch & Science

Install Deepspot M

skills CLI
$ npx skills add K-Dense-AI/scientific-agent-skills --skill deepspot-m -a claude-code

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

GitHub CLI
$ gh skill install K-Dense-AI/scientific-agent-skills deepspot-m --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/K-Dense-AI/scientific-agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/deepspot-m .claude/skills/deepspot-m && 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
deepspot-m
GitHub stars
48k
Used in
1 other repo
Token cost
~2.5k tokens
SKILL.md length
1,007 words
Files
3 (incl. references)
Skills in repo
153
Repo updated
First seen
Licence
PolyForm-Noncommercial-1.0.0

At a glance

Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M.

  • Works in 2 steps: Open and request access. → Once access is granted, authenticate the…
  • Tasks that involve Bioinformatics
  • SKILL.md covers Overview, Licensing, Installation and Model access, plus 9 more sections
  • Calls uv and hf; reaches huggingface.co; needs HF_TOKEN

What it does

Deepspot M is an agent skill from K-Dense-AI/scientific-agent-skills. Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Used for predicted log1p-CPM expression from 224x224 tiles at about 20x, querying the released protein-coding gene panel by symbol, and whole-slide prediction after resolution-aware tiling with histolab.

Its SKILL.md is about 2.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files, including reference files (for example `references/api.md` and `references/whole_slide.md`). Compatibility notes: Requires deepspotm 1.0.0, Python =3.10 and PyTorch; network and approved Hugging Face access for initial gated weight download. CPU supported; CUDA optional…

It sits in Research & Science, covering Bioinformatics and Slides and decks. The repository describes itself as: Turn any AI agent into an AI Scientist. The 1 Agent Skills library for science, used by 250,000+ scientists worldwide. 177 ready-to-use validated skills plus 100+ scientific…

When your agent uses it

  • Tasks that involve Bioinformatics
  • Tasks that involve Slides and decks

Example prompts

  • “Use the deepspot-m skill to generate transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M”
  • “/deepspot-m”

Requirements

  • Python 3
  • Compatibility (from SKILL.md): Requires deepspotm 1.0.0, Python >=3.10 and PyTorch; network and approved Hugging Face access for initial gated weight download. CPU supported; CUDA optional. Optional histolab 0.7.0 tiling requires a separate Python 3.10/3.11 environment and OpenSlide. AnnData is needed for H5AD export.
  • Pre-approved tools (allowed-tools): Read, Write, Edit, Bash

Workflow steps

2 steps, taken from the first numbered list in SKILL.md.

  1. Open and request access.
  2. Once access is granted, authenticate the machine that will download them

What it can do on your machine

Read from SKILL.md and the folder at commit 92ace75. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves these tools, so the agent can use them without asking each time:

    • Read
    • Write
    • Edit
    • Bash

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Shell commands in SKILL.md call:

    • uv
    • hf

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • huggingface.co

    Also links to:

    • doi.org
    • github.com
    • pypi.org

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names these keys or tokens, usually read from environment variables:

    • HF_TOKEN

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

  • Compatibility

    Requires deepspotm 1.0.0, Python >=3.10 and PyTorch; network and approved Hugging Face access for initial gated weight download. CPU supported; CUDA optional. Optional histolab 0.7.0 tiling requires a separate Python 3.10/3.11 environment and OpenSlide. AnnData is needed for H5AD export.

    From compatibility in the SKILL.md frontmatter.

Context cost

Deepspot M loads about 2.5k tokens when it runs, and up to ~7k if it reads all its reference files. Until then it costs about 78 tokens; SKILL.md has 1,007 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
~2.5k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~7k

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: notes

The automated check noted patterns worth knowing about, such as sudo or a known installer.

  • NotePre-approves every shell command (allowed-tools: Bash)SKILL.md
    allowed-tools: Read, Write, Edit, Bash

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

Its licence (PolyForm-Noncommercial-1.0.0) doesn't allow us to republish the file, so here is its outline and opening line. It has 1,007 words (~2,485 tokens).

“DeepSpot-M is a multimodal foundation model that maps a 224x224 H&E histology tile to spatial gene expression in log1p-CPM. The output is virtual spatial transcriptomics: one value per queried gene per tile, laid out on the grid the tiles came…”

— opening of SKILL.md by K-Dense-AI, PolyForm-Noncommercial-1.0.0
name
deepspot-m
allowed-tools
Read, Write, Edit, Bash
compatibility
Requires deepspotm 1.0.0, Python >=3.10 and PyTorch; network and approved Hugging Face access for initial gated weight download. CPU supported; CUDA optional. Optional histolab 0.7.0 tiling requires a separate Python 3.10/3.11 environment and OpenSlide. AnnData is needed for H5AD export.
license
PolyForm-Noncommercial-1.0.0
metadata.version
1.2
metadata.skill-author
Ratschlab, ETH Zurich
metadata.last-reviewed
2026-09-30

Read the full SKILL.md on GitHub

Files

SKILL.md and 2 other files (references) in skills/deepspot-m of K-Dense-AI/scientific-agent-skills.

  • SKILL.md
  • references/api.md
  • references/whole_slide.md

Open the folder on GitHubat commit 92ace75

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 K-Dense-AI/scientific-agent-skills, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Deepspot M 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.

Deepspot M compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Deepspot M this skillK-Dense-AI/scientific-agent-skills48k1 repos~2.5kAutomated safety check: NotesPolyForm-Noncommercial-1.0.0
Single2spatial Spatial MappingFreedomIntelligence/OpenClaw-Medical-Skills3.1k2 repos~994Automated safety check: PassNone
Bio Spatial Transcriptomics Spatial Data IoFreedomIntelligence/OpenClaw-Medical-Skills3.1k1 repos~2kAutomated safety check: PassNone
Bio Spatial Transcriptomics Spatial MultiomicsFreedomIntelligence/OpenClaw-Medical-Skills3.1k1 repos~1.6kAutomated safety check: PassNone
Bio Spatial Transcriptomics High Resolution BinningGPTomics/bioSkills1.2k1 repos~3.7kAutomated safety check: PassMIT
Bio Spatial Transcriptomics Spatial DomainsGPTomics/bioSkills1.2k1 repos~4.8kAutomated safety check: PassMIT

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  • Single2spatial Spatial Mapping

    FreedomIntelligence/OpenClaw-Medical-Skills

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

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  • Bio Spatial Transcriptomics Spatial Data Io

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  • Bio Spatial Transcriptomics Spatial Multiomics

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  • Bio Spatial Transcriptomics High Resolution Binning

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  • Bio Spatial Transcriptomics Spatial Domains

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  • Spatial Transcriptomics Tutorials With Omicverse

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Categories

Questions about Deepspot M

What does Deepspot M do?

Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Deepspot M is an agent skill from K-Dense-AI/scientific-agent-skills. Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M.

When should I use Deepspot M?

Deepspot M fits situations like: tasks that involve Bioinformatics; tasks that involve Slides and decks.

How do I install Deepspot M in Claude Code?

Run `npx skills add K-Dense-AI/scientific-agent-skills --skill deepspot-m -a claude-code`. Or copy the skill folder (skills/deepspot-m in K-Dense-AI/scientific-agent-skills) into .claude/skills/deepspot-m in your project. Claude Code loads it when a task matches its description.

How do I install Deepspot M in Codex?

Run `npx skills add K-Dense-AI/scientific-agent-skills --skill deepspot-m -a codex`. Or copy the skill folder (skills/deepspot-m in K-Dense-AI/scientific-agent-skills) into .agents/skills/deepspot-m in your project. Codex loads it when a task matches its description.

Can I use Deepspot M 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 K-Dense-AI/scientific-agent-skills --skill deepspot-m -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/deepspot-m, .gemini/skills/deepspot-m, .github/skills/deepspot-m and .opencode/skills/deepspot-m in your project.

What does Deepspot M need to run?

Going by SKILL.md and its folder, Deepspot M needs the command-line tools its instructions call (uv and hf) and credentials named HF_TOKEN. Our summary lists: Python 3. Its frontmatter pre-approves these tools: Read, Write, Edit, Bash. Compatibility (from SKILL.md): Requires deepspotm 1.0.0, Python >=3.10 and PyTorch; network and approved Hugging Face access for initial gated weight download. CPU supported; CUDA optional. Optional histolab 0.7.0 tiling requires a separate Python 3.10/3.11 environment and OpenSlide. AnnData is needed for H5AD export..

Does Deepspot M access the network?

SKILL.md names 4 domains. In commands or code: huggingface.co; the agent is likely to contact it when it follows the instructions. As links in the text: doi.org, github.com and pypi.org. This is read from the text; nothing was executed.

Is Deepspot M safe to install?

Our automated static check of SKILL.md found notes only (pre-approves every shell command (allowed-tools: bash)), nothing it rates as a warning. It is not a guarantee. Review the folder before installing.

What licence does Deepspot M use?

Deepspot M is published under the PolyForm-Noncommercial-1.0.0 licence (declared in SKILL.md).

How many tokens does Deepspot M use?

About 2.5k tokens (SKILL.md is roughly 9.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 4.6k tokens, read only when the agent opens those files.

What are the alternatives to Deepspot M?

Skills that share tags, products or a category with Deepspot M: Single2spatial Spatial Mapping (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Bio Spatial Transcriptomics Spatial Data Io (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Bio Spatial Transcriptomics Spatial Multiomics (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars) and Bio Spatial Transcriptomics High Resolution Binning (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 Deepspot M?

K-Dense-AI (a GitHub organization) maintains it in K-Dense-AI/scientific-agent-skills, which has 48,215 GitHub stars. The repository holds 153 skills in this directory. The repository was last updated on October 5, 2026.

Source: K-Dense-AI/scientific-agent-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.