Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Towards the construction of a virtual yeast.

Nature·2026

Same author

Disruption of dynactin complex function in intellectual disability.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Frequency-Domain Transformation of cfDNA End-Motif Profiles Enhances Robust Cancer Detection.

Genes·2026

Same author

JAK/STAT signaling pathway in the spleen and liver during early pregnancy in ewes.

Reproductive biology·2026

Same author

Efficient preservation of old methane-derived organic carbon in deep-sea surface sediments.

Nature communications·2026

Same author

CauFinder: Steering Cell-State and Phenotype Transitions by Causal Disentanglement Learning.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026

Same journal

Bifacial Perovskite Solar Cells by Lamination Approach With a PEDOT:PSS/d-Sorbitol Blended Adhesion Layer.

Small methods·2026

Same journal

Dual-Sided Interface Optimization Enables High-Brightness All-Solution-Processed ZnMgO-Based Green Perovskite QLEDs.

Small methods·2026

Same journal

Intelligent Sensing Gloves Enabled by Liquid Metal Atomized Spraying for Shared Human-Machine Interaction.

Small methods·2026

Same journal

Confinement-Amplified Tritiated Water Clean-Up in Functionalized Graphene Oxide Nanochannels.

Small methods·2026

Same journal

Optimizing the Development Process in Direct Photolithography for Efficient PeLEDs.

Small methods·2026

Same journal

Fluorinated Diluents Enable Crowded Solvation Environments to Form Anion-Rich SEIs for High-Performance Potassium-Ion Batteries.

Small methods·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 6, 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

Spatially Aware Domain Adaptation Enables Cell Type Deconvolution from Multi-Modal Spatially Resolved

Lequn Wang^1,2,3, Xiaosheng Bai², Chuanchao Zhang²

¹Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.

|December 3, 2024

Summary

This summary is machine-generated.

SpaDA integrates multi-modal data for spatial transcriptomics, accurately mapping cell types within tissues. This novel method improves understanding of cellular heterogeneity and spatial domains.

Keywords:

deconvolution graph representation self‐expressive variational autoencoder spatial distribution alignment spatial domains detection

More Related Videos

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Related Experiment Videos

Last Updated: Jun 6, 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

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Area of Science:

Genomics
Computational Biology
Bioinformatics

Background:

Spatially Resolved Transcriptomics (SRT) enables detailed tissue analysis.
Current methods lack multi-modal integration for spatial cell type deconvolution.
Understanding cellular heterogeneity in spatial contexts remains a challenge.

Purpose of the Study:

To develop a novel method, SpaDA, for integrating multi-modal SRT data.
To accurately estimate the spatial distribution of cell types by modeling transcriptomics, histology, and spatial locations.
To enhance the understanding of cellular heterogeneity in spatial contexts.

Main Methods:

SpaDA employs a spatially aware domain adaptation approach.
Utilizes a self-expressive variational autoencoder and deep spatial distribution alignment.
Integrates multi-modal SRT data with single-cell RNA sequencing (scRNA-seq) data.

Main Results:

SpaDA accurately estimates cell type spatial distribution and composition.
Outperforms existing methods in cell type deconvolution and spatial domain identification across platforms.
Successfully identifies spatially colocalized cell types and marker genes in low-quality regions, demonstrated on mouse cerebellum data.

Conclusions:

SpaDA provides a powerful framework for multi-modal SRT data analysis.
Advances the understanding of complex biological systems through integrated spatial analysis.
Enables accurate cell type deconvolution and spatial domain identification.