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

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 ultra-structure 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. 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. Introduction Assessing the structure of the brain is critical to better understanding its normal and abnormal functioning. 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 [1, 2]. Quantitative analysis of 3D-EM data, such as morphological assessment of ultrastructure, spatial distribution or connectivity of cells, requires the instance segmentation of individual ultrastructural components [3, 4, 5]. Performing this segmentation manually is tedious, if not impossible, due to the large size and enormous number of components in typical 3D-EM data.