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 CHENyiru3/AI-Skills-Collections --skill spatialdatagit clone --depth 1 https://github.com/CHENyiru3/AI-Skills-CollectionsWrote 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/chenyiru3/ai-skills-collections/spatialdata)<a href="https://agentmods.dev/skills/chenyiru3/ai-skills-collections/spatialdata"><img src="https://agentmods.dev/badge/skills/chenyiru3/ai-skills-collections/spatialdata/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/chenyiru3/ai-skills-collections/spatialdata"><img src="https://agentmods.dev/badge/skills/chenyiru3/ai-skills-collections/spatialdata.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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 | $0.00030 | $0.00476 |
| Opus 5.5 | $0.00012 | $0.00190 |
| Sonnet 5.5 | $0.00006 | $0.00095 |
| Haiku 4.5 | $0.00003 | $0.00048 |
Grade A, and why
spatialdata 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 6d 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.
What it actually says
SpatialData: Spatial Omics Framework
Overview
SpatialData is a Python framework that provides a unified representation for various spatial omics data types. It enables interoperability between different spatial platforms and analysis tools within the scverse ecosystem.
When to Use This Skill
This skill should be used when:
- Working with multiple spatial data types
- Need to integrate different spatial platforms
- Using the scverse ecosystem for analysis
- Creating pipelines across spatial modalities
- Requiring standardized spatial data formats
Quick Start
Installation
pip install spatialdata
# With all dependencies
pip install spatialdata[all]
Basic Usage
from spatialdata import SpatialData
import scanpy as sc
# Load data
sdata = SpatialData.read("data.zarr")
# Access different modalities
sdata.table # Obs table
sdata.shapes # Shapes (spots, polygons)
sdata.images # Images
Data Types
Supported Platforms
- 10X Visium
- 10X Xenium
- Vizgen MERFISH
- NanoString CosMX
- Akoya CODEX
- ImcData
Integration
With Scanpy
# Convert to AnnData for scanpy analysis
adata = sdata.table.to_adata()
# Run scanpy analysis
sc.pp.pca(adata)
sc.pp.neighbors(adata)
sc.tl.umap(adata)
# Add back to SpatialData
sdata.table = adata
With Squidpy
import squidpy as sq
# Use squidpy functions with SpatialData
Best Practices
- Use Zarr format: Best for large spatial data
- Check coordinate systems: Ensure consistent transformations
- Document metadata: Record acquisition parameters
Additional Resources
- Documentation: https://spatialdata.scverse.org/
- GitHub: https://github.com/scverse/spatialdata
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.
- 6d ago First seen · 97 lines · 30 tokens per session scan A df9e641c30d7
spatialdata is a skill published in the GitHub repository CHENyiru3/AI-Skills-Collections (1 stars, last pushed 7d ago), licensed MIT. It adds 30 tokens to every session and 476 once invoked, about $0.0001 per session on Opus 5.5. 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 2026-10-02.
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