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spatial-transcriptomics

spatial-transcriptomics is a skill for Claude Code, Codex from zamushwani/biomedical-ai-skills. It costs 0 tokens per session (11,824 once invoked), scanned A, original, MIT.

A guide for processing and analysing spatial transcriptomics data, which records gene activity together with where it was measured in tissue. It covers sequencing-based and imaging-based platforms, using Python and R tools.

In plain words
What is it for?
Use it to process Visium, Slide-seq, Stereo-seq, Xenium, MERSCOPE, or CosMx data, detect quality problems, find spatially variable genes, and convert between spatial data formats.
Why use it?
It helps choose suitable loading, quality-control, normalization, and analysis steps for different spatial data formats and measurement scales.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

not rated 1repo 1mo ago A scan 0 tokens original MIT

Good fit Use it to process Visium, Slide-seq, Stereo-seq, Xenium, MERSCOPE, or CosMx data, detect quality problems, find spatially variable genes, and convert between spatial data formats.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/zamushwani/biomedical-ai-skills/spatial-transcriptomics
View source ↗ zamushwani/biomedical-ai-skills
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add zamushwani/biomedical-ai-skills --skill spatial-transcriptomics
Clone the repo
git clone --depth 1 https://github.com/zamushwani/biomedical-ai-skills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for spatial-transcriptomics

README.md
[![agentmods](https://agentmods.dev/badge/skills/zamushwani/biomedical-ai-skills/spatial-transcriptomics/github.svg)](https://agentmods.dev/skills/zamushwani/biomedical-ai-skills/spatial-transcriptomics)
Your own site
<a href="https://agentmods.dev/skills/zamushwani/biomedical-ai-skills/spatial-transcriptomics"><img src="https://agentmods.dev/badge/skills/zamushwani/biomedical-ai-skills/spatial-transcriptomics/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for spatial-transcriptomics

Your own site · 80×15
<a href="https://agentmods.dev/skills/zamushwani/biomedical-ai-skills/spatial-transcriptomics"><img src="https://agentmods.dev/badge/skills/zamushwani/biomedical-ai-skills/spatial-transcriptomics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 0 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 11,824 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00000 $0.11824
Opus 5.5 $0.00000 $0.04730
Sonnet 5.5 $0.00000 $0.02365
Haiku 4.5 $0.00000 $0.01182

Measured 2mo ago against content hash e8d118807737, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

spatial-transcriptomics scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

The scan reads SKILL.md. This mod also ships 4 executable files (tests/run_all.py, tests/validate_loading.py, tests/validate_neighbors.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/spatial-transcriptomics/SKILL.md · 1,080 lines

How it starts

The opening of the file, as written. The whole thing — 1,080 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Spatial Transcriptomics

Processing and analysis of spatially resolved transcriptomics across sequencing-based (Visium, Visium HD, Slide-seq, Stereo-seq) and imaging-based (Xenium, MERSCOPE, CosMx) platforms. Covers loading, QC, normalization, and spatially variable gene detection. Dual-language: Python (squidpy/SpatialData) and R (SpatialExperiment/Seurat v5).

When to Use This Skill

Activate when the user requests:

  • Visium or Visium HD data loading and quality control
  • Xenium, MERSCOPE, CosMx, or Stereo-seq processing
  • Spatial quality control and artifact detection
  • Spatially variable gene (SVG) detection
  • Spatial autocorrelation (Moran's I, Geary's C)
  • Conversion between spatial data containers
  • Any analysis where transcript measurements carry coordinates

Platform Types

The single most important distinction. It determines every downstream choice.

Sequencing-based (spot/bin resolution, whole transcriptome):
  Visium        55 um spots, ~1-10 cells per spot, ~18k genes
  Visium HD     2 um bins (binned to 8/16 um), subcellular grid, whole transcriptome
  Slide-seq V2  10 um beads
  Stereo-seq    220 nm DNB, binned
  -> Spots mix cell types. You need DECONVOLUTION.

Imaging-based (single-cell/subcellular, targeted panel):
  Xenium        ~5k genes max (Prime 5K), segmented cells
  MERSCOPE      ~500-1000 genes
  CosMx         ~1000-6000 genes
  -> Cells are already segmented. You need CELL TYPING, not deconvolution.
     Segmentation quality is the dominant error source.

Inputs

Platform Format Reader
Visium Space Ranger outs/ (h5 + tissue_positions.csv + images) squidpy.read.visium, VisiumIO::TENxVisium
Visium HD Space Ranger outs/ with binned_outputs/, tissue_positions.parquet spatialdata_io.visium_hd, VisiumIO::TENxVisiumHD
Xenium Xenium Onboard Analysis output bundle spatialdata_io.xenium, XeniumIO::TENxXenium
MERSCOPE Vizgen output (cell_by_gene.csv, cell_metadata.csv) spatialdata_io.merscope
CosMx NanoString flat files spatialdata_io.cosmx, readCosmxSXE
Stereo-seq STOmics GEF/GEM (v7.x only) spatialdata_io.stereoseq

Read the full file on GitHub · 1,080 lines

Files

What ships with it

6 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 2mo ago First seen · 1,080 lines · 0 tokens per session scan A e8d118807737

Subscribe to this mod's changes

spatial-transcriptomics is a skill published in the GitHub repository zamushwani/biomedical-ai-skills (1 stars, last pushed 1mo ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 11,824 tokens. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

Analytics and metricsDESeq2Scientificai-agentai-skillsbioinformaticscancer-genomicscancer-research
Related

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spatial-transcriptomics next to 6 skills from other repositories
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