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spatial-register

Performs spatial registration and multi-slice alignment for spatial transcriptomics data using Python.

155|26|Updated Mar 14, 2026
Search Tags:#alignment#spatial transcriptomics#registration#PASTE#Procrustes#multi-slice
One-click install
npx skills add https://github.com/TianGzlab/OmicsClaw --skill spatial-register
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: spatial-register
Source: https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/spatial-register
Command: npx skills add https://github.com/TianGzlab/OmicsClaw --skill spatial-register

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires scanpy, scipy, numpy, pandas, matplotlib, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the alignment of spatial coordinates across multiple tissue slices, which is crucial for integrating and analyzing serial sections or replicate experiments in spatial transcriptomics.

Core Features & Use Cases

  • Multi-slice Alignment: Aligns N slices to a reference slice using methods like Procrustes or PASTE.
  • Coordinate Transformation: Updates spatial coordinates to reflect the aligned positions.
  • Use Case: Aligning serial sections of a tumor to reconstruct a 3D spatial map or comparing gene expression patterns across replicate tissue samples.

Quick Start

Align my spatial transcriptomics slices using the PASTE method.

Frequently Asked Questions about spatial-register

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I align multiple spatial transcriptomics slices for 3D reconstruction?▼

To align multiple spatial transcriptomics slices, you can use this Skill to perform multi-slice spatial registration. It aligns N tissue sections to a reference slice and updates spatial coordinates to reconstruct 3D spatial maps.

What is the difference between Procrustes and PASTE methods for spatial transcriptomics registration?▼

Procrustes and PASTE are two supported methods for coordinate alignment in spatial transcriptomics. Procrustes performs standard shape alignment, while PASTE specifically optimizes spatial transcriptomics data integration across serial sections.

Can I use scanpy and scipy for spatial transcriptomics multi-slice alignment?▼

Yes, this Skill requires scanpy and scipy for core multi-slice alignment functionality. It processes spatial transcriptomics data within the scanpy ecosystem and uses scipy for underlying coordinate transformations.

Do I need the paste-bio package to align serial tissue sections?▼

No, the paste-bio package is optional. This Skill supports the PASTE method for spatial transcriptomics alignment but also includes a Procrustes method, allowing you to align serial tissue sections without installing paste-bio.

When do I need spatial registration for multi-slice tissue samples?▼

You need spatial registration when integrating serial tissue sections or replicate experiments in spatial transcriptomics. It is crucial for comparing gene expression patterns across samples and reconstructing 3D spatial maps of tissues like tumors.

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