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

DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

Improving Translational Accuracy

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

Improving Translational Accuracy

Improving Translational Accuracy

Electron Microscope Tomography and Single-particle Reconstruction

Electron Microscope Tomography and Single-particle Reconstruction

Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...

You might also read

Related Articles

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

Sort by

Same author

HisCMCL: Cross-Modal Contrastive Learning with Hierarchical Multi-Scale Fusion for Spatial Expression Prediction.

Bioinformatics (Oxford, England)·2026

Same author

Active Cough Sputum Clearance Grading System: A Novel Predictor of Early Tracheostomy in Patients With Acute Traumatic Cervical Spinal Cord Injury.

World neurosurgery·2025

Same author

SpaBatch: Deep Learning-Based Cross-Slice Integration and 3D Spatial Domain Identification in Spatial Transcriptomics.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2025

Same author

SpaICL: image-guided curriculum strategy-based graph contrastive learning for spatial transcriptomics clustering.

Briefings in bioinformatics·2025

Same author

Improving cell-type composition inference in spatial transcriptomics with SpaDAMA.

PLoS computational biology·2025

Same author

The impact of sedation and analgesia scores on prognosis in critically ill sepsis patients with sepsis-associated encephalopathy: a retrospective analysis.

Frontiers in neurology·2025

Same journal

Salt priming coordinates transcriptional and epigenetic states for enhanced salt tolerance in mung bean (Vigna radiata).

Communications biology·2026

Same journal

A male-derived volatile sex pheromone in Caenorhabditis nematodes identified through its mimicry by a predator.

Communications biology·2026

Same journal

Revalidation of Manis aurita based on integrative genomic and morphological evidence.

Communications biology·2026

Same journal

Presenilin-1 controls glycolysis and identity of pancreatic beta cells.

Communications biology·2026

Same journal

Base editing-derived models of human WDR34 and WDR60 disease alleles replicate retrograde intraflagellar transport (IFT) and hedgehog signaling defects.

Communications biology·2026

Same journal

Butterflies with low thermoregulatory capacity show greatest upwards range shifts along an elevational gradient.

Communications biology·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 16, 2026

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Published on: September 5, 2025

SpaCross deciphers spatial structures and corrects batch effects in multi-slice spatially resolved transcriptomics.

Donghai Fang¹, Wenwen Min²

¹School of Information Science and Engineering, Yunnan University, Kunming, China.

Communications Biology

|October 1, 2025

Summary

This summary is machine-generated.

SpaCross, a new deep learning framework, improves spatial domain identification in Spatially Resolved Transcriptomics (SRT) by enhancing pattern recognition and multi-slice integration. It accurately maps tissue architecture and developmental trajectories across different samples and stages.

More Related Videos

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

Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics

Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics

Published on: May 3, 2024

Related Experiment Videos

Last Updated: Jan 16, 2026

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Published on: September 5, 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

Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics

Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics

Published on: May 3, 2024

Area of Science:

Computational Biology
Genomics
Bioinformatics

Background:

Spatially Resolved Transcriptomics (SRT) integrates gene expression with spatial data for tissue analysis.
Current SRT domain identification methods face challenges in unsupervised learning, latent space supervision, and multi-slice integration consistency.
Balancing local spatial continuity and global semantic consistency remains a key hurdle.

Purpose of the Study:

To introduce SpaCross, a deep learning framework designed to enhance spatial pattern recognition and cross-slice consistency in SRT.
To address limitations in existing unsupervised spatial domain identification methods.
To enable robust multi-slice integration and accurate reconstruction of tissue architecture.

Main Methods:

SpaCross utilizes a cross-masked graph autoencoder for gene expression reconstruction and spatial relationship preservation.
A cross-masked latent consistency module enforces implicit constraints on latent representations for improved robustness.
An adaptive spatial-semantic graph structure dynamically integrates local and global contextual information for multi-slice analysis.

Main Results:

SpaCross outperforms thirteen state-of-the-art methods on single-slice SRT datasets.
Demonstrates robust batch effect correction and preservation of biologically meaningful spatial architectures in multi-slice integration.
Successfully integrates embryonic mouse tissues across developmental stages, identifying conserved and stage-specific structures like the dorsal root ganglion.

Conclusions:

SpaCross offers a comprehensive framework for advanced spatial domain identification in SRT.
The method effectively reconstructs developmental trajectories and identifies key transcriptional transitions in cardiac maturation.
SpaCross advances the analysis of tissue architecture and developmental processes using multi-slice SRT data.