gACSON software for automated segmentation and morphology analyses of myelinated axons in 3D electron microscopy

TL;DR

gACSON is a free, MATLAB-based software tool that enables automated and manual segmentation, visualization, and morphological analysis of myelinated axons in 3D electron microscopy brain tissue images, facilitating ultrastructural studies.

Contribution

The paper introduces gACSON, a novel software that combines automated segmentation with manual correction for detailed 3D analysis of myelinated axons in EM data.

Findings

Myelinated axons' diameter decreased in TBI rats five months post-injury.

gACSON effectively segments and analyzes axonal and myelin morphology.

The software is freely available for the neuroscience community.

Abstract

Background and Objective: Advances in electron microscopy (EM) now allow three-dimensional (3D) imaging of hundreds of micrometers of tissue with nanometer-scale resolution, providing new opportunities to study the ultrastructure of the brain. In this work, we introduce a freely available Matlab-based gACSON software for visualization, segmentation, assessment, and morphology analysis of myelinated axons in 3D-EM volumes of brain tissue samples. Methods: The software is equipped with a graphical user interface (GUI). It automatically segments the intra-axonal space of myelinated axons and their corresponding myelin sheaths and allows manual segmentation, proofreading, and interactive correction of the segmented components. gACSON analyzes the morphology of myelinated axons, such as axonal diameter, axonal eccentricity, myelin thickness, or g-ratio. Results: We illustrate the use of the software by segmenting and analyzing myelinated axons in six 3D-EM volumes of rat somatosensory cortex after sham surgery or traumatic brain injury (TBI). Our results suggest that the equivalent diameter of myelinated axons in somatosensory cortex was decreased in TBI animals five months after the injury. Conclusions: Our results indicate that gACSON is a valuable tool for visualization, segmentation, assessment, and morphology analysis of myelinated axons in 3D-EM volumes. It is freely available at https://github.com/AndreaBehan/g-ACSON under the MIT license.