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

You might also read

Related Articles

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

Sort by
Same author

RepliSage: a stochastic graph-based framework for 3D chromatin modeling across the cell cycle.

Nucleic acids research·2026
Same author

Calcium Buffering in Astrocytes and Its Relevance for Experimental Data Interpretation and Computational Modeling.

Journal of neurochemistry·2026
Same author

De novo design of anticancer 4-thiazolidinone derivatives: a generative framework shaped by activity cliffs.

Journal of cheminformatics·2026
Same author

Artificial Intelligence in the prediction of 3D chromatin structure and gene regulation.

Progress in molecular biology and translational science·2026
Same author

Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.

Genome research·2026
Same author

Correction to: GPX4 is a key ferroptosis regulator orchestrating T cells and CAR-T-cells sensitivity to ferroptosis.

Cancer immunology, immunotherapy : CII·2026

Related Experiment Video

Updated: Oct 14, 2025

Author Spotlight: Optimizing Dendritic Spine Analysis for Balanced Manual and Automated Assessment in the Hippocampus CA1 Apical Dendrites
07:45

Author Spotlight: Optimizing Dendritic Spine Analysis for Balanced Manual and Automated Assessment in the Hippocampus CA1 Apical Dendrites

Published on: September 27, 2024

2.5K

3dSpAn: An interactive software for 3D segmentation and analysis of dendritic spines.

Nirmal Das1,2, Ewa Baczynska3,4, Monika Bijata3

  • 1Department of CSE, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata, 700032, India.

Neuroinformatics
|November 7, 2021
PubMed
Summary

We developed 3dSpAn software to segment and analyze dendritic spine morphology in 3D. This tool addresses key challenges in neurobiology research for accurate quantitative morphological feature extraction.

Keywords:
Dendritic spinesInteractive softwareQuantitative analysis.Synaptic plasticityThree-dimensional segmentation

More Related Videos

Three-dimensional Quantification of Dendritic Spines from Pyramidal Neurons Derived from Human Induced Pluripotent Stem Cells
10:18

Three-dimensional Quantification of Dendritic Spines from Pyramidal Neurons Derived from Human Induced Pluripotent Stem Cells

Published on: October 10, 2015

11.7K
Automatic Identification of Dendritic Branches and their Orientation
06:08

Automatic Identification of Dendritic Branches and their Orientation

Published on: September 17, 2021

2.0K

Related Experiment Videos

Last Updated: Oct 14, 2025

Author Spotlight: Optimizing Dendritic Spine Analysis for Balanced Manual and Automated Assessment in the Hippocampus CA1 Apical Dendrites
07:45

Author Spotlight: Optimizing Dendritic Spine Analysis for Balanced Manual and Automated Assessment in the Hippocampus CA1 Apical Dendrites

Published on: September 27, 2024

2.5K
Three-dimensional Quantification of Dendritic Spines from Pyramidal Neurons Derived from Human Induced Pluripotent Stem Cells
10:18

Three-dimensional Quantification of Dendritic Spines from Pyramidal Neurons Derived from Human Induced Pluripotent Stem Cells

Published on: October 10, 2015

11.7K
Automatic Identification of Dendritic Branches and their Orientation
06:08

Automatic Identification of Dendritic Branches and their Orientation

Published on: September 17, 2021

2.0K

Area of Science:

  • Neuroscience
  • Biophysics
  • Computational Biology

Background:

  • Accurate segmentation and morphological analysis of dendritic spines are crucial for understanding neuronal function and plasticity.
  • Existing methods face challenges in isolating individual spines and quantifying their complex 3D structures.

Purpose of the Study:

  • To introduce 3dSpAn, a novel software tool for automated 3D segmentation and quantitative morphological analysis of dendritic spines.
  • To validate the software's performance across various imaging modalities and conditions.

Main Methods:

  • Development of 3dSpAn software based on a 3D multi-scale opening algorithm.
  • Implementation of four modules: Preprocessing/ROI selection, Intensity thresholding/seed selection, Multi-scale segmentation, and Morphological feature extraction.
  • Testing with in vitro, ex vivo (confocal microscopy), and in vivo (two-photon microscopy) imaging data.

Main Results:

  • Demonstrated successful segmentation and quantitative morphological analysis of dendritic spines under diverse imaging conditions.
  • Evaluated the influence of adjustable parameters on segmentation results and assessed user reproducibility and accuracy.
  • Provided a qualitative comparison against a commercial benchmark software.

Conclusions:

  • 3dSpAn provides a robust and versatile solution for 3D dendritic spine analysis.
  • The software facilitates accurate quantitative morphological feature extraction, aiding neurobiological research.
  • 3dSpAn is freely available for non-commercial use, promoting wider scientific accessibility.