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deepspot-m

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

Skill by K-Dense-AI

IndexedPolyForm-Noncommercial-1.0.0★ 54,411
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Install

Works with Claude Code, Claude apps, Codex, Cursor, Gemini CLI, GitHub Copilot, VS Code, OpenCode, Goose, Windsurf. Read the repository before you give any tool access to your data.

npx agentmarket install skill/k-dense-ai-deepspot-m

Asks which of your tools to add it to (Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI, Claude Desktop) and shows the change first. See https://agentmart.dev/cli.

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About

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.

Use cases: presentations

Reviews

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Permissions

What this skill can do and what it asks for, from its SKILL.md. Checked Oct 25, 2026.

Tools
No tools found
Secrets
None asked for
Install scripts
None found

Network hosts it talks to 1

  • codeload.github.com · found in install command

Files it touches

  • ~/.claude/skills/deepspot-m

Tools it pre-approves 4

From allowed-tools in SKILL.md: the agent may use these without asking you each time.

  • Read
  • Write
  • Edit
  • Bash

What's inside

Skill name
deepspot-m
Description
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.
License
PolyForm-Noncommercial-1.0.0
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.
Allowed tools
Read, Write, Edit, Bash
Metadata
version: 1.2 · skill-author: Ratschlab, ETH Zurich · last-reviewed: 2026-09-30
Instructions
209 lines in SKILL.md · view on GitHub

Before installing

  • Pre-approves any shell command

Files (3)

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

The license isn't open source, so the instructions aren't shown here. Read SKILL.md on GitHub

More from K-Dense-AI/scientific-agent-skills

Signals

Stars
54,411
Forks
4,797
Open issues
8
Last commit (this folder)
Oct 1, 2026 (27 days ago)
Last release
Oct 1, 2026 (27 days ago)

From GitHub (fetched Oct 24, 2026).

Details

Version
1.2
License
PolyForm-Noncommercial-1.0.0
Repository
github.com/K-Dense-AI/scientific-agent-skills
Website
arxiv.org/abs/2609.00065
First seen
Oct 24, 2026
Last checked
Oct 24, 2026
Source
GitHubgithub-graphql

More from K-Dense-AI

Cite this page

deepspot-m skill. Agent Mart. https://agentmart.dev/skills/k-dense-ai-deepspot-m (last updated 2026-10-24)