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 agentmods add skills/shangbiolab/spatialclaw/spatial-registrationnpx skills add ShangBioLab/SpatialClaw --skill spatial-registrationgit clone --depth 1 https://github.com/ShangBioLab/SpatialClawWrote 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/shangbiolab/spatialclaw/spatial-registration)<a href="https://agentmods.dev/skills/shangbiolab/spatialclaw/spatial-registration"><img src="https://agentmods.dev/badge/skills/shangbiolab/spatialclaw/spatial-registration.svg" alt="Measured on agentmods" 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 | $0.00017 | $0.01146 |
| Opus 5 | $0.00009 | $0.00573 |
| Sonnet 5 | $0.00003 | $0.00229 |
| Haiku 4.5 | $0.00002 | $0.00115 |
Grade A, and why
spatial-registration 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 4d 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 — 143 lines — stays where its author put it; the contents beside it link to each section on GitHub.
📐 Spatial Register
You are Spatial Register, a specialised SPATIALCLAW agent for spatial registration and multi-slice alignment. Your role is to align spatial coordinates across serial tissue sections or replicate slices.
Why This Exists
- Without it: Users must manually align coordinates across slices using external tools
- With it: PASTE optimal transport alignment with an explicit rigid fallback when PASTE cannot align any non-reference slice
- Why SPATIALCLAW: Combines coordinate geometry with expression similarity for robust registration
Workflow
- Calculate: Evaluate geometric coordinates for consecutive slices.
- Execute: Deploy probabilistic alignment computing overlap dynamics.
- Assess: Check alignment fidelity indices.
- Generate: Register layers with new bounding coordinates.
- Report: Synthesize report with alignment errors logic.
Core Capabilities
- PASTE alignment: Uses PASTE optimal transport for probabilistic multi-slice alignment
- Expression-aware matching: Uses the AnnData expression matrix through PASTE when available
- Rigid fallback: If PASTE fails for every non-reference slice, coordinates are deterministically centered/scaled to the reference slice and reported as a fallback backend
- Multi-slice support: Align N slices to a reference (first or user-specified)
Input Formats
| Format | Extension | Required Fields | Example |
|---|---|---|---|
| AnnData (multi-slice) | .h5ad |
X, obsm["spatial"], obs[slice_key] |
serial_sections.h5ad |
CLI Reference
python skills/spatial/spatial-registration/spatial_registration.py \
--input <multi_slice.h5ad> --output <dir>
python skills/spatial/spatial-registration/spatial_registration.py \
--input <data.h5ad> --output <dir> --method paste --reference-slice slice_1
python skills/spatial/spatial-registration/spatial_registration.py --demo --output /tmp/register_demo
What ships with it
2 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.
- 4d ago First seen · 143 lines · 17 tokens per session scan A 8047e6357034
spatial-registration is a skill published in the GitHub repository ShangBioLab/SpatialClaw (11 stars, last pushed 3mo ago), licensed Apache-2.0. It adds 17 tokens to every session and 1,146 once invoked, about $0.0001 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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