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Related Experiment Video

Updated: Aug 1, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

Alignment of spatial transcriptomics data using diffeomorphic metric mapping.

Kalen Clifton^1,2, Manjari Anant^1,3, Gohta Aihara^1,2

¹Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21211.

Biorxiv : the Preprint Server for Biology

|April 24, 2023

Summary

This summary is machine-generated.

STalign is a new computational tool that aligns spatial transcriptomics datasets, overcoming challenges in comparing gene expression across different samples and technologies. This method improves spatial correspondence and enables detailed analysis of tissue composition.

Keywords:

LDDMM common coordinate framework diffeomorphic mapping spatial alignment spatial transcriptomics

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Last Updated: Aug 1, 2025

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Published on: July 6, 2022

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis

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Published on: June 27, 2020

Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis

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Area of Science:

Computational Biology
Genomics
Bioinformatics

Background:

Spatial transcriptomics (ST) technologies offer high-throughput gene expression profiling within tissue sections.
Comparing ST data across different sections, samples, and technologies is currently challenging due to distortions and variations.
Standard alignment methods struggle with non-linear deformations and partial tissue matching.

Conclusions:

STalign provides a powerful solution for aligning spatial transcriptomics data, enhancing cross-dataset comparability.
The tool facilitates the integration of ST data with 3D anatomical references.
STalign supports advanced analyses of tissue composition and spatial organization across anatomical structures.