Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Determining the Plane of Cell Division02:13

Determining the Plane of Cell Division

Positioning the cell division plane is a critical step during development and cell differentiation, particularly during mitosis when the plane is essential for determining the size of the two daughter cells. The cell division plane is perpendicular to the plane of chromosome segregation, but different types of organisms have different cell division mechanisms to suit their morphology and function. 
Animal cells
In animal cells, the cleavage furrow forms along the plane of cell division starting...
Determining the Plane of Cell Division02:13

Determining the Plane of Cell Division

Positioning the cell division plane is a critical step during development and cell differentiation, particularly during mitosis when the plane is essential for determining the size of the two daughter cells. The cell division plane is perpendicular to the plane of chromosome segregation, but different types of organisms have different cell division mechanisms to suit their morphology and function. 
Animal cells
In animal cells, the cleavage furrow forms along the plane of cell division starting...
Three-Dimensional Microscopy in Microbiology01:28

Three-Dimensional Microscopy in Microbiology

Three-dimensional imaging techniques are essential in cell biology, allowing researchers to visualize intricate cellular structures with high resolution. Two prominent methods, Differential Interference Contrast Microscopy (DIC) and Confocal Scanning Laser Microscopy (CSLM), provide distinct advantages for imaging live and thick specimens, respectively.Differential Interference Contrast MicroscopyDIC microscopy enhances contrast in transparent, unstained samples by converting phase...

You might also read

Related Articles

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

Sort by
Same author

Analysis of whole genome sequencing and plasma metabolomics unveil genetic determinants and clinical implications for human health.

Nature communications·2026
Same author

Comprehensive review and assessment of multi-species splicing variant prediction: task-specific deep learning models and genomic foundation models.

Briefings in bioinformatics·2026
Same author

Clinical Evaluation of the Revised Biological and Clinical Staging Criteria for Alzheimer Disease in China.

Neurology·2026
Same author

A hierarchical multi-scale framework for schizophrenia: integrating symptom networks, functional circuits, and molecular pathways.

Molecular psychiatry·2026
Same author

SOFisher: reinforcement learning-guided experiment designs for spatial omics.

Nature communications·2026
Same author

Bridging molecules and connectome: network biomarkers guided by neurotransmitter architecture in major depressive disorder.

Translational psychiatry·2026
Same journal

Spatio-DARLIN enables robust and efficient in situ lineage tracing in mice at single-cell resolution.

Nature methods·2026
Same journal

EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control.

Nature methods·2026
Same journal

Cloud-based microscope enables live neuroimaging for 24 h and beyond with worldwide access.

Nature methods·2026
Same journal

Deep molecular profiling in three dimensions.

Nature methods·2026
Same journal

3D pathology-guided microdissection.

Nature methods·2026
Same journal

Challenges and recommendations in establishing national human diversity genomic projects.

Nature methods·2026
See all related articles

Related Experiment Video

Updated: Jun 16, 2026

Three-dimensional Imaging of Bacterial Cells for Accurate Cellular Representations and Precise Protein Localization
06:33

Three-dimensional Imaging of Bacterial Cells for Accurate Cellular Representations and Precise Protein Localization

Published on: October 29, 2019

10.6K

Bridging the dimensional gap from planar spatial transcriptomics to 3D cell atlases.

Senlin Lin1,2,3, Zhikang Wang1,2,4, Yan Cui1,2

  • 1Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.

Nature Methods
|December 31, 2025
PubMed
Summary
This summary is machine-generated.

SpatialZ creates detailed 3D cell atlases from sparse spatial transcriptomics data by generating virtual tissue slices. This computational framework enables high-resolution 3D mapping of molecular landscapes in organs and tissues.

More Related Videos

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

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

Published on: July 6, 2022

5.3K
Mining Spatial Transcriptomics Datasets using DeepSpaceDB
10:16

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Published on: September 5, 2025

613

Related Experiment Videos

Last Updated: Jun 16, 2026

Three-dimensional Imaging of Bacterial Cells for Accurate Cellular Representations and Precise Protein Localization
06:33

Three-dimensional Imaging of Bacterial Cells for Accurate Cellular Representations and Precise Protein Localization

Published on: October 29, 2019

10.6K
Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

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

Published on: July 6, 2022

5.3K
Mining Spatial Transcriptomics Datasets using DeepSpaceDB
10:16

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Published on: September 5, 2025

613

Area of Science:

  • Computational biology
  • Genomics
  • Bioinformatics

Background:

  • Spatial transcriptomics (ST) advances tissue architecture understanding but struggles with 3D atlas construction due to sparse sampling and high costs.
  • Existing 2D ST methods create data gaps, limiting comprehensive 3D organ organization insights.
  • Bridging these gaps is crucial for high-resolution 3D cell atlases.

Purpose of the Study:

  • To introduce SpatialZ, a computational framework for generating dense 3D cell atlases from planar ST data.
  • To enable the creation of virtual slices between experimentally measured sections, filling data gaps.
  • To provide a versatile tool for high-resolution 3D spatial molecular landscape analysis.

Main Methods:

  • SpatialZ computationally generates virtual 2D slices from sparse experimental ST data.
  • The framework operates at single-cell resolution and is independent of gene coverage limitations.
  • Validation involved applying SpatialZ to BRAIN Initiative Cell Census Network data and imaging mass cytometry data.

Main Results:

  • SpatialZ successfully constructed a 3D hemisphere atlas with over 38 million cells.
  • The framework accurately preserves cell identities, gene expression, and spatial relationships.
  • Demonstrated extensibility by analyzing 3D spatial gradients in human breast cancer using imaging mass cytometry data.

Conclusions:

  • SpatialZ enables the construction of dense 3D cell atlases from planar ST data, overcoming current limitations.
  • The generated atlases offer unprecedented 3D resolution for exploring spatial molecular architectures.
  • SpatialZ facilitates novel analyses, including in silico sectioning and 3D mapping, advancing biological discovery.