Image-guided alignment of consecutive multi-modal tissue slides
Cell Reports Methods, pp. 101575
Abstract
We present COAST (consecutive multi-omics alignment of spatial tissues), a method to reliably physically align consecutive tissue sections to produce a unified multi-modal molecular dataset suitable for downstream applications. COAST relies exclusively on the images associated with spatial data, eliminating the need for common molecular features or prior annotations. We demonstrate the effectiveness of COAST using spatial transcriptomics slides from different technologies, tissues, and resolutions, in which it achieves performance comparable to established uni-modal alignment tools. Applying COAST to spatial transcriptomics and metabolomics/lipidomics tissue sections from a mouse model of ischemia-reperfusion injury allowed the investigation of lipid/metabolite features of transcriptionally defined cell types. Overall, COAST offers a streamlined and integrative solution for multi-modal spatial data alignment.
Authors 9
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Benedetta Manzato Aachen
Leiden University Medical Center · Novo Nordisk Foundation Center for Stem Cell Medicine
Affiliation as printed
Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZA, the Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden 2333ZA, the Netherlands
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Claudio Novella-Rausell Aachen
Leiden University Medical Center · Novo Nordisk Foundation Center for Stem Cell Medicine
Affiliation as printed
Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZA, the Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden 2333ZA, the Netherlands
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Gangqi Wang Aachen
Fudan University · Leiden University Medical Center · Children's Hospital of Fudan University
Affiliation as printed
Department of Internal Medicine (Nephrology) & Einthoven Laboratory of Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden 2333ZA, the Netherlands; Children's Hospital of Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China
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Leiden University Medical Center
Affiliation as printed
Center for Proteomics and Metabolomics (CPM), Leiden University Medical Center, Leiden 2333ZA, the Netherlands
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Rosalie G. J. Rietjens Aachen
Leiden University Medical Center · Novo Nordisk Foundation Center for Stem Cell Medicine
Affiliation as printed
The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden 2333ZA, the Netherlands; Department of Internal Medicine (Nephrology) & Einthoven Laboratory of Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
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Marleen E Jacobs Aachen
Leiden University Medical Center · Novo Nordisk Foundation Center for Stem Cell Medicine
Affiliation as printed
The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden 2333ZA, the Netherlands; Department of Internal Medicine (Nephrology) & Einthoven Laboratory of Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
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Sébastien J. Dumas Aachen
Inserm · Leiden University Medical Center · Institut des Maladies Métaboliques et Cardiovasculaires · Université de Toulouse · Novo Nordisk Foundation Center for Stem Cell Medicine
Affiliation as printed
The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden 2333ZA, the Netherlands; Department of Internal Medicine (Nephrology) & Einthoven Laboratory of Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden 2333ZA, the Netherlands; National Institute of Health and Medical Research (INSERM), UMR 1297, Institute of Metabolic and Cardiovascular Diseases, University of Toulouse, Toulouse, France
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Ton J. Rabelink Aachen
Leiden University Medical Center · Novo Nordisk Foundation Center for Stem Cell Medicine
Affiliation as printed
The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden 2333ZA, the Netherlands; Department of Internal Medicine (Nephrology) & Einthoven Laboratory of Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
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Leiden University Medical Center · Delft University of Technology
Affiliation as printed
Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZA, the Netherlands; Delft Bioinformatics Lab, Delft University of Technology, Delft 2628XE, the Netherlands. Electronic address: a.mahfouz@lumc.nl
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