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

Three-Dimensional Microscopy in Microbiology01:28

Three-Dimensional Microscopy in Microbiology

915
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...
915

You might also read

Related Articles

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

Sort by
Same author

Methicillin-resistant Staphylococcus aureus extracellular vesicles induced IL-8 dependent proliferation in oral squamous cell carcinoma.

Journal of advanced research·2026
Same author

Quantifying the counter-intuitive effects of vaccination by coupling the transmission dynamics of COVID-19 and the evolution of human behaviors.

Journal of theoretical biology·2026
Same author

Single-threshold-guided adaptive cancer therapy with partial-cycle treatment: A mechanistic and reinforcement learning analysis.

PLoS computational biology·2026
Same author

Cu<sup>2+</sup> Doping-Induced Microstructural Engineering of V<sub>2</sub>O<sub>5</sub> Cathodes for High-Performance Zinc-Ion Hybrid Supercapacitors with Enhanced Energy and Rate Capability.

Langmuir : the ACS journal of surfaces and colloids·2026
Same author

Activation of the p62/Keap1/Nrf2 Pathway Protects Against Ferroptosis in Cerebral Ischemia-Reperfusion Injury.

Journal of integrative neuroscience·2026
Same author

Persistent soil resistome expansion following bacterial inoculation despite successful antibiotic bioremediation.

Journal of hazardous materials·2026

Related Experiment Video

Updated: May 6, 2026

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data
05:12

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data

Published on: January 16, 2019

11.2K

3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape.

Qi Wang, Biao Tang, Lifu Song

  • 1Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100190, People's Republic of China. liuxueting_cn@hotmail.com.

BMC Bioinformatics
|November 15, 2013
PubMed
Summary
This summary is machine-generated.

Biological data visualization is challenging due to its large scale. A new 3D Cytoscape Client/Server (3DScapeCS) plugin offers enhanced interpretation of complex networks, improving biological data analysis.

More Related Videos

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

414.6K
Visualization and Quantification of High-Dimensional Cytometry Data using Cytofast and the Upstream Clustering Methods FlowSOM and Cytosplore
06:01

Visualization and Quantification of High-Dimensional Cytometry Data using Cytofast and the Upstream Clustering Methods FlowSOM and Cytosplore

Published on: December 12, 2019

10.1K

Related Experiment Videos

Last Updated: May 6, 2026

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data
05:12

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data

Published on: January 16, 2019

11.2K
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

414.6K
Visualization and Quantification of High-Dimensional Cytometry Data using Cytofast and the Upstream Clustering Methods FlowSOM and Cytosplore
06:01

Visualization and Quantification of High-Dimensional Cytometry Data using Cytofast and the Upstream Clustering Methods FlowSOM and Cytosplore

Published on: December 12, 2019

10.1K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Data Visualization

Background:

  • Exponential growth of biological data from sources like protein-protein interaction (PPI) networks, genome scaffolding, and mass spectrometry (MS) molecular networking necessitates advanced visualization.
  • Conventional 2D visualization tools struggle to efficiently represent and interpret the complexity and scale of modern biological datasets.

Purpose of the Study:

  • To develop an advanced visualization tool for large-scale biological networks.
  • To overcome the limitations of traditional 2D methods in interpreting complex, multi-dimensional biological data.

Main Methods:

  • Development of a 3D Cytoscape Client/Server (3DScapeCS) plugin.
  • Integration of Cytoscape for data interpretation and UbiGraph for 3D visualization.
  • Application of the plugin to five diverse case studies involving complex biological networks.

Main Results:

  • The 3DScapeCS plugin effectively visualizes large-scale networks with multiple crossed connections.
  • The added third dimension aids in accommodating, visualizing, and distinguishing complex network structures.
  • Case studies demonstrated the plugin's capability in handling diverse and large biological datasets.

Conclusions:

  • 3DScapeCS proves useful for visualizing complex biological data, including multilevel graph layouts and time-course data animation.
  • The tool facilitates insightful conclusions from experimental data through advanced visualization features.
  • Parallel visualization capabilities enhance the interpretation of intricate biological networks.