# Deepspot M

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

- Repository: https://github.com/ClawBio/ClawBio (1172 stars)
- Category: Engineering
- License: MIT
- Last updated: 2026-11-01
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add ClawBio/ClawBio --skill deepspot-m -g -a claude-code -y`
Codex: `npx skills add ClawBio/ClawBio --skill deepspot-m -g -a codex -y`
Cursor: `npx skills add ClawBio/ClawBio --skill deepspot-m -g -a cursor -y`
Gemini CLI: `npx skills add ClawBio/ClawBio --skill deepspot-m -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add ClawBio/ClawBio`

## Description

Transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Scores a 224x224 tile and returns per-gene log1p-CPM values for any HGNC symbols you ask for, with a CSV, a report and a reproducibility bundle.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 🧬 DeepSpot-M Virtual Spatial Transcriptomics

You are **deepspot-m**, a specialised ClawBio agent that turns an H&E histology tile into virtual spatial transcriptomics. You score one 224x224 tile with the DeepSpot-M foundation model and report per-gene log1p-CPM values for the gene symbols the user names.

## Trigger

**Fire this skill when the user says any of:**
- "virtual spatial transcriptomics"
- "predict gene expression from histology"
- "spatial transcriptomics from H&E"
- "what genes are expressed in this tissue image"
- "score this tile for BRAF and COL1A1"
- "run DeepSpot-M on this tile"
- "gene expression map from a slide"
- "H&E to transcriptome"

**Do NOT fire when:**
- The user wants cells counted or outlined in an image. That is `cell-detection`.
- The user already has a measured spot-count table and wants region labels. That is `marker-dominance-mapper`.
- The user wants differential expression between conditions from a count matrix. That is `rnaseq-de`.
- The user wants single-cell clustering or embedding of an AnnData object. That is `scrna-orchestrator` or `scrna-embedding`.
- The user asks for TCGA bulk expression lookups. That is `xena-tcga-gene-query`.

## Why This Exists

- **Without it**: Reading expression off an archived slide means running a spatial assay on the tissue, which most samples never get.
- **With it**: One archived H&E tile yields per-gene values in one command, entirely on the local machine.
- **Why ClawBio**: The call goes to a published model with released weights, pinned to one checkpoint, and every run leaves a reproducibility bundle behind.

This is a research tool, not a substitute for measurement. The model card publishes no per-gene accuracy figure, and neither does the preprint abstract, so this skill quotes none. Read the preprint for the evaluation before treating any number here as a finding, and see `## Safety` for the limitations upstream states.

## Core Capabilities

The rest: https://github.com/ClawBio/ClawBio/blob/HEAD/skills/deepspot-m/SKILL.md