Batch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns

Batch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns

Abstract Spatial transcriptomics facilitates gene expression analysis of cells in their spatial anatomical context. Batch effects hinder visualization of gene spatial patterns across samples. We present the Crescendo algorithm to correct for batch effects at the gene expression level and enable accu...

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Main Authors: Nghia Millard, Jonathan H. Chen, Mukta G. Palshikar, Karin Pelka, Maxwell Spurrell, Colles Price, Jiang He, Nir Hacohen, Soumya Raychaudhuri, Ilya Korsunsky
Format: Article
Language:English
Published: BMC 2025-02-01
Series:Genome Biology
Subjects:
Single-cell
Spatial transcriptomics
Batch correction
Crescendo
Patterns
Ligand-receptor interactions
Online Access:https://doi.org/10.1186/s13059-025-03479-9
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https://doi.org/10.1186/s13059-025-03479-9

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