  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.
