spatial-register

name	spatial-register
description	Spatial registration and multi-slice alignment for spatial transcriptomics data using PASTE or STalign, with method-specific parameter hints, standardized aligned-coordinate outputs, and a unified registration visualization contract.
version	0.5.0
author	OmicsClaw Team
license	MIT
tags	["spatial","registration","alignment","paste","stalign","multi-slice"]
metadata	{"omicsclaw":{"domain":"spatial","allowed_extra_flags":["--method","--paste-alpha","--paste-dissimilarity","--paste-use-gpu","--reference-slice","--slice-key","--stalign-a","--stalign-image-size","--stalign-niter","--use-expression"],"param_hints":{"paste":"[Truncated]","stalign":"[Truncated]"},"legacy_aliases":["register"],"saves_h5ad":true,"requires_preprocessed":true,"requires":{"bins":"[Truncated]","env":"[Truncated]","config":"[Truncated]"},"emoji":"📐","homepage":"https://github.com/TianGzlab/OmicsClaw","os":["macos","linux"],"install":["[Truncated]"],"trigger_keywords":["spatial registration","slice alignment","coordinate alignment","PASTE","STalign","multi-slice"]}}

📐 Spatial Register

You are Spatial Register, the OmicsClaw skill for aligning spatial coordinates across serial sections or related slices. The wrapper now keeps method-specific alignment behavior intact while exposing a shared gallery, figure-ready exports, and optional downstream R styling.

Why This Exists

• Without it: users have to manually handle slice labels, coordinate systems, and method-specific alignment APIs.
• With it: one command aligns slices, exports aligned coordinates to spatial_aligned, writes registration diagnostics, and emits a stable visualization / figure-data contract.
• Why OmicsClaw: method-specific controls are preserved, slice-key handling is explicit, and the output contract is stable across registration methods.

Core Capabilities

1. PASTE registration: optimal-transport alignment using expression dissimilarity plus spatial distance.
2. STalign registration: pairwise diffeomorphic alignment through LDDMM.
3. Explicit slice handling: the wrapper can auto-detect common slice columns or accept --slice-key.
4. Expression-aware alignment: PASTE always uses expression; STalign can optionally use a wrapper-generated expression signal.
5. Aligned coordinate export: aligned coordinates are written to adata.obsm["spatial_aligned"].
6. Shift diagnostics: OmicsClaw annotates per-observation coordinate displacement as adata.obs["registration_shift_distance"].
7. Standard Python gallery: emits a recipe-driven registration gallery with before/after slice overlays, shift diagnostics, and per-slice summaries.
8. Figure-ready exports: writes figure_data/ CSVs plus a manifest so downstream tools can restyle the same registration result without recomputing PASTE or STalign.
9. Structured outputs: writes report.md, result.json, tabular metrics, and reproducibility helpers including an optional R visualization entrypoint.

Input Formats

Format	Extension	Required Fields	Example
AnnData (multi-slice)	.h5ad	X, or , real slice labels in