Overview
deepspot-m is an open-source data skill for Claude Code and compatible agents, published by K-Dense-AI. Its author describes it as: “Generate transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Use when you need spatial gene expression in log1p-CPM for 224x224 tiles at about 20x, want to query protein-coding genes…”. The project has 40k stars on GitHub and is available under the MIT license. Add it to your setup with `git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/deepspot-m`.
What deepspot-m does
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 from.
Best for
What’s inside
The SKILL.md for deepspot-m is organised into these sections:
- Overview
- Licensing
- Installation
- Model access
- Quick start
- Tile requirements
- Keep the dependency optional
- Embedding sources
- Whole slide workflow
- Common use cases
- Detailed references
- Primary sources
Installation
Add deepspot-m to your agent with:
git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/deepspot-mReview a skill’s source before installing it — skills can instruct your agent to run commands. This command comes from the skill’s public repository, which is the source of truth for setup steps. New to skills? Read how to install Claude Code skills.
Supported agents
Neither the skill nor its repository names a specific agent. It uses the SKILL.md format, which several agents can load — check the repository for any agent-specific requirements.
License
deepspot-m is published under the MIT license.
Strengths
- Clear MIT license — safe to read and adapt within its terms
- Ships in K-Dense-AI/scientific-agent-skills, an established project with 40,410 GitHub stars
- Actively maintained — repository updated in the last 30 days
- Its repository gained 6,589 GitHub stars over the last 13 days
Author
Topics
Frequently asked questions
- What does deepspot-m do?
- Generate transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Use when you need spatial gene expression in log1p-CPM for 224x224 tiles at about 20x, want to query protein-coding genes by symbol instead of a fixed panel, or want to run prediction across a whole slide after tiling with histolab.
- How do I install deepspot-m?
- Run git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/deepspot-m in your agent, then reload your skills. Review the source at https://github.com/K-Dense-AI/scientific-agent-skills before installing.
- Is deepspot-m free to use?
- Yes. deepspot-m is free and open source under the MIT license, so you can read, run, and adapt it within that license's terms.
- Where does deepspot-m come from?
- deepspot-m ships inside K-Dense-AI/scientific-agent-skills, a repository that contains 42 catalogued skills in total. The repository's 40,410 GitHub stars apply to that whole collection, not to this skill on its own.