ArticleScientific reports2018
AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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84 citing papers in PubMed.
- Volume electron microscopy reveals oligodendrocyte axon selection patterns and spatial assembly of myelin and nodes.iScience · 2026Article
- LMNB1 reduction is a potential therapeutic strategy in a mouse model of autosomal dominant leukodystrophy.JCI insight · 2026Article
- BasNet: Attention U-Net-Based Automated Axon Segmentation in Bielschowsky Silver-Stained Histology.Neuroinformatics · 2026Article
- Evaluating the Influence of Injury-Induced Microstructural Variations on the Efficacy of a Diffusion MRI-Derived Axon Diameter Surrogate.Magnetic resonance in medicine · 2026Article
- Automated segmentation of neurons and spinal cord structures in immunofluorescence images using SpineDL.Scientific reports · 2026Article
- Computational Morphometry of Peripheral Nerves: A Pipeline Perspective on Reproducibility and Generalization.Neuroinformatics · 2026Review
- Comparison of Deep Learning Tools for Optic Nerve Axon Quantification Finds Limited Generalizability Upon Independent Validation.Bioengineering (Basel, Switzerland) · 2026Article
- Ultrastructural analysis of human uncinate fasciculus with coherent anti-Stokes Raman spectroscopy.Biophotonics discovery · 2026Article
- Sphingolipid-neutralizing molecular therapy reduces psychosine cytotoxicity in Krabbe disease.iScience · 2026Article
- Comparison of Deep Learning Tools for Optic Nerve Axon Quantification Finds Limited Generalizability on Independent Validation.bioRxiv : the preprint server for biology · 2026Article
- Brain-wide mapping of oligodendrocyte organization, oligodendrogenesis, and myelin injury.Cell · 2026Article
- Self-Assembling Peptide Hydrogels Support Stromal Vascular Fraction Viability to Promote In Vivo Nerve Regeneration.Advanced healthcare materials · 2026Article
- AxoMetric platform facilitates rapid and unbiased automated quantification of axon regeneration in tissue sections.Cell reports methods · 2026Article
- Inhibited oligodendrogenesis impairs attention and motivation in adult mice regardless of repeated mild traumatic brain injury.Frontiers in behavioral neuroscience · 2026Article
- Modeling strategies in non-invasive spinal stimulation: perspectives on state-of-the-art.Frontiers in human neuroscience · 2026Review
- Article
- Advances in multiscale myelin imaging: from classical histology to functional insights.Frontiers in cellular neuroscience · 2026Review
- Vincristine-induced brain toxicity is reduced with prevention of peripheral axon degeneration in Sarm1 knockout mice.Acta neuropathologica communications · 2025Article
- MyeliMetric: A Python-Based Toolbox for Standardized G-Ratio Analysis of Axon-Myelin Integrity.ASN neuro · 2025Article
- Evolutionary expansion of the corticospinal system is linked to dexterity inbioRxiv : the preprint server for biology · 2025Article
24 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
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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 a 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 .
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