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.
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-squidpy-spatialgit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-SkillsWrote 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.
[](https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-squidpy-spatial)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-squidpy-spatial"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-squidpy-spatial/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.
<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-squidpy-spatial"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-squidpy-spatial.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00201 | $0.02392 |
| Opus 5 | $0.00101 | $0.01196 |
| Sonnet 5 | $0.00040 | $0.00478 |
| Haiku 4.5 | $0.00020 | $0.00239 |
Grade A, and why
alterlab-squidpy-spatial 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 10d ago.
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.
How it starts
The opening of the file, as written. The whole thing — 168 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Squidpy: Spatial Transcriptomics
Squidpy is the scverse toolkit for spatially-resolved omics, built on AnnData and
SpatialData. It answers questions a non-spatial scRNA-seq pipeline cannot: which
cell types sit next to which (neighborhood enrichment), how cell-type pairs
co-occur across distance (co-occurrence), which genes vary across tissue space
(Moran's I / spatially variable genes), and what ligand-receptor signalling is
plausible (ligrec). This skill does the spatial analysis; it hands non-spatial
QC/clustering to alterlab-scanpy and spot deconvolution to alterlab-scvi-tools.
When to Use This Skill
Use when the request involves:
- Spatial transcriptomics / spatially-resolved omics on Visium, Visium HD, Xenium, MERFISH/MERSCOPE, or CosMx data.
- Building a spatial neighbor graph and running neighborhood enrichment, co-occurrence, interaction matrix, Ripley's statistics, or centrality scores.
- Finding spatially variable genes via Moran's I (
spatial_autocorr) or Sepal. - Ligand-receptor analysis in a spatial context (
ligrec). - Reading platform output into AnnData/SpatialData and choosing the right
coord_typefor the platform.
Does NOT Trigger
| Request | Route to |
|---|---|
| Non-spatial scRNA-seq QC, normalization, PCA/UMAP, Leiden clustering, marker genes | alterlab-scanpy |
| Spot deconvolution / mapping cell types to Visium spots (destVI, Tangram), probabilistic batch correction/integration | alterlab-scvi-tools (see its references/models-spatial.md) |
Building/slicing/concatenating .h5ad AnnData objects, layer & obsm wrangling (no spatial analysis) |
alterlab-anndata |
| RNA-velocity / trajectory dynamics | alterlab-scvelo |
| Bulk RNA-seq differential expression from a count matrix | alterlab-pydeseq2 |
| Raw FASTQ → expression matrix (read alignment/quantification) | alterlab-rnaseq-quant |
| Diversity / ecology statistics on a feature table | alterlab-scikit-bio |
What ships with it
5 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.
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.
- 10d ago First seen · 168 lines · 201 tokens per session scan A 65aac736120d
alterlab-squidpy-spatial is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (66 stars, last pushed 5d ago), licensed MIT. It adds 201 tokens to every session and 2,392 once invoked, about $0.0010 per session on Opus 5. 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 2026-08-30.
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