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🧬 DeepSpot-M Virtual Spatial Transcriptomics · clawbio | DecimalAI

scienceby clawbio

🧬 DeepSpot-M Virtual Spatial Transcriptomics

clawbio/deepspot-m

Source clawbio/clawbio ↗License NOASSERTION

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.

SkillScore86Maintained

Automatic

Research pack

Last verified 9/26/2026

What it changes

Passed 15 of 17 test cases with the skill, and 3 of 17 without it.

Without skill18%

With skill86%

Checks it passed that the model alone missed

States that tile images must measure exactly 224x224 pixels.
States 0.05 as the default minimum saturation threshold value.
States that scgpt is the default gene embedding source setting.

and 18 more in the full report

15 fixed4 passed either way3 still failing0 broke

Pass-rate lift: +68 pp
Tokens: +200%
Agent turns: 0%
Response time: -66%

Model gemini-3.6-flashMeasured 9/26/2026v119 of 22 cases passed with skill · 17 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/clawbio-deepspot-m/SKILL.md https://app.decimal.ai/s/clawbio-deepspot-m/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add clawbio-deepspot-m, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/clawbio-deepspot-m/ and pins it in .decimal/skills.lock

decimalai skills add clawbio-deepspot-m

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/clawbio-deepspot-m/SKILL.md https://app.decimal.ai/s/clawbio-deepspot-m/SKILL.md

Raw file: /s/clawbio-deepspot-m/SKILL.md ↗ · machine-readable summary at /s/clawbio-deepspot-m.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 13 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 13

Prompt

In `tables/gene_expression.csv`, what is the exact value populated in the `provenance` column when running a standard model prediction versus a demo fixture run?

What was checked, without and with the skill
Checked	Without skill	With skill
States that standard model prediction rows set provenance to model_prediction in the CSV output.	Missed	Passed
States that demo fixture runs set provenance to demo_fixture in the CSV output.	Missed	Passed

case-18 · gemini-3.6-flash · 9/26/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md308 linessingle file

🧬 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

Score a tile: Map one 224x224 H&E tile to per-gene log1p-CPM values.
Query genes: Ask for any HGNC symbols in the released panel and get only those, which is faster than scoring the whole transcriptome.
Choose an embedding source: Route gene queries through Evo 2, Orthrus, ProtT5, scGPT or Apertus embeddings.
Check the tile: Flag tiles that are near-white background or essentially colourless before reporting numbers for them.
Report: Write report.md, result.json, a gene CSV and a reproducibility bundle.

Scope

Track record

Benchmark

15 / 17

test cases passed, vs 3 / 17 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v5 — 8/25/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

clawbio / clawbio

skills/deepspot-m/SKILL.md

View on GitHub ↗

License MITImported 8/25/2026Version v1

Other skills for the same job

Published skills whose descriptions closely match this one, with their headline benchmark lift.

k-dense-ai/deepspot-mGenerate 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.Close match+67 pp pass-rate lift

More skills from the same source and nearby in the registry, with their headline benchmark lift.

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See it in action

What's inside

🧬 DeepSpot-M Virtual Spatial Transcriptomics

Trigger

Why This Exists

Core Capabilities

Scope

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

Related skills