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

Patterns of Muscle Health in Single- and Multi-Site Chronic Pain: A UK Biobank Normative Modeling Study.

medRxiv : the preprint server for health sciences·2026
Same author

Optimization in Sparse 2D to Dense 3D Weakly Supervised Learning: Application to Multi-Label Segmentation of Large ex vivo MRI Data.

ArXiv·2026
Same author

Charting Cervical Spinal Cord Morphometry Across the Lifespan.

bioRxiv : the preprint server for biology·2026
Same author

Spinal cord imaging for multiple sclerosis: Advances, priorities, and opportunities.

Multiple sclerosis (Houndmills, Basingstoke, England)·2026
Same author

Automatic multiple sclerosis lesion segmentation in the spinal cord using 3 T and 7 T MP2RAGE images.

Multiple sclerosis and related disorders·2026
Same author

Segmentation of spinal rootlets across MRI contrasts with RootletSeg.

Scientific reports·2026

Related Experiment Video

Updated: Mar 15, 2026

Automatic Identification of Dendritic Branches and their Orientation
06:08

Automatic Identification of Dendritic Branches and their Orientation

Published on: September 17, 2021

2.3K

AxonSeg: Open Source Software for Axon and Myelin Segmentation and Morphometric Analysis.

Aldo Zaimi1, Tanguy Duval1, Alicja Gasecka2

  • 1Institute of Biomedical Engineering, Polytechnique Montreal Montreal, QC, Canada.

Frontiers in Neuroinformatics
|September 6, 2016
PubMed
Summary

AxonSeg is a new open-source software for automatically segmenting axons and myelin in histology images. It extracts key morphometric data, aiding neuroscience research and MRI technique validation.

Keywords:
axondiscriminant analysisg-ratiographical user interfacehistologymicroscopymyelinsegmentation

More Related Videos

Author Spotlight: Unveiling the Molecular Basis of Pain Perception and Neuropathic Pain
05:28

Author Spotlight: Unveiling the Molecular Basis of Pain Perception and Neuropathic Pain

Published on: August 9, 2024

1.8K
Analysis of Multidimensional Microscopy Data Using Cell-ACDC
06:17

Analysis of Multidimensional Microscopy Data Using Cell-ACDC

Published on: November 7, 2025

672

Related Experiment Videos

Last Updated: Mar 15, 2026

Automatic Identification of Dendritic Branches and their Orientation
06:08

Automatic Identification of Dendritic Branches and their Orientation

Published on: September 17, 2021

2.3K
Author Spotlight: Unveiling the Molecular Basis of Pain Perception and Neuropathic Pain
05:28

Author Spotlight: Unveiling the Molecular Basis of Pain Perception and Neuropathic Pain

Published on: August 9, 2024

1.8K
Analysis of Multidimensional Microscopy Data Using Cell-ACDC
06:17

Analysis of Multidimensional Microscopy Data Using Cell-ACDC

Published on: November 7, 2025

672

Area of Science:

  • Neuroscience
  • Biomedical Imaging
  • Computational Biology

Background:

  • Accurate segmentation of axon and myelin is crucial for understanding nervous system structure and function.
  • Existing software often has limited interfaces or modality-specific applications, hindering broad adoption.

Purpose of the Study:

  • To introduce AxonSeg, a novel, versatile software for automatic axon and myelin segmentation.
  • To enable extraction of essential morphometric parameters like axon diameter, density, and g-ratio.
  • To validate AxonSeg across diverse microscopy modalities.

Main Methods:

  • AxonSeg employs a pipeline including image pre-processing, discriminant analysis for parameter selection, and automatic segmentation.
  • It utilizes a MATLAB-based graphical user interface (GUI) for intuitive operation.
  • The software adapts to various imaging modalities, including optical microscopy (OM), scanning electron microscopy (SEM), and CARS microscopy.

Main Results:

  • AxonSeg successfully performed automatic axon and myelin segmentation on histology images.
  • Morphometric data, including axon diameter distribution, density, and g-ratio, were accurately extracted.
  • Segmentation results were validated against manual segmentations across multiple imaging techniques.

Conclusions:

  • AxonSeg offers a fully automatic and adaptable solution for histology image analysis.
  • The software facilitates high-throughput analysis, supporting large-scale neuroscience research.
  • AxonSeg is freely available as open-source software, promoting accessibility and collaboration.