AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks

TL;DR

AxonDeepSeg is an open-source deep learning tool that accurately segments axons and myelin in microscopy images, facilitating quantitative analysis of nervous tissue microstructure across species.

Contribution

It introduces a convolutional neural network-based method with ready-to-use models for axon and myelin segmentation, simplifying the process and reducing user parameter tuning.

Findings

High pixel-wise accuracy across species and microscopy modalities

Effective segmentation of full spinal cord slices

Open-source availability for broad research use

Abstract

Segmentation of axon and myelin from microscopy images of the nervous system provides useful quantitative information about the tissue microstructure, such as axon density and myelin thickness. This could be used for instance to document cell morphometry across species, or to validate novel non-invasive quantitative magnetic resonance imaging techniques. Most currently-available segmentation algorithms are based on standard image processing and usually require multiple processing steps and/or parameter tuning by the user to adapt to different modalities. Moreover, only few methods are publicly available. We introduce AxonDeepSeg, an open-source software that performs axon and myelin segmentation of microscopic images using deep learning. AxonDeepSeg features: (i) a convolutional neural network architecture; (ii) an easy training procedure to generate new models based on manually-labelled data and (iii) two ready-to-use models trained from scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Results show high pixel-wise accuracy across various species: 85% on rat SEM, 81% on human SEM, 95% on mice TEM and 84% on macaque TEM. Segmentation of a full rat spinal cord slice is computed and morphological metrics are extracted and compared against the literature. AxonDeepSeg is freely available at https://github.com/neuropoly/axondeepseg