AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks
This provides a tool for researchers in neuroscience and medical imaging to automate axon and myelin segmentation, reducing the need for manual tuning and improving accessibility, though it is incremental as it applies existing deep learning methods to a specific domain.
The authors tackled the problem of segmenting axons and myelin from microscopy images, which is crucial for quantifying tissue microstructure, by introducing AxonDeepSeg, an open-source software using convolutional neural networks that achieved high pixel-wise accuracies, such as 95% on mice TEM and 84% on macaque TEM.
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