ArticleFrontiers in neuroinformatics2016
AxonSeg: Open Source Software for Axon and Myelin Segmentation and Morphometric Analysis.
Article in Frontiers in neuroinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Can MRI measure myelin? Systematic review, qualitative assessment, and meta-analysis of studies validating microstructural imaging with myelin histology.NeuroImage · 2021Pooled it
- Computational Morphometry of Peripheral Nerves: A Pipeline Perspective on Reproducibility and Generalization.Neuroinformatics · 2026Review
- Impact of tongue exercise on hypoglossal axis survival, structure, and output in a rodent model of hypoglossal motor neuron degeneration.Journal of neurophysiology · 2026Article
- Prenatal valproic acid on the basis of gestational diabetes also induces autistic behavior and disrupts myelination and oligodendroglial maturation slightly in offspring.Translational psychiatry · 2025Article
- Self-supervised segmentation and characterization of fiber bundles in anatomic tracing data.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Developmental origin of oligodendrocytes determines their function in the adult brain.Nature neuroscience · 2024Article
- NRV: An open framework for in silico evaluation of peripheral nerve electrical stimulation strategies.PLoS computational biology · 2024Article
- Vibrational spectroscopy and multiphoton microscopy for label-free visualization of nervous system degeneration and regeneration.Biophysical reviews · 2024Review
- NRV: An open framework forbioRxiv : the preprint server for biology · 2024Article
- CellWalker: a user-friendly and modular computational pipeline for morphological analysis of microscopy images.Bioinformatics (Oxford, England) · 2023Article
- AimSeg: A machine-learning-aided tool for axon, inner tongue and myelin segmentation.PLoS computational biology · 2023Article
- AxoNet 2.0: A Deep Learning-Based Tool for Morphometric Analysis of Retinal Ganglion Cell Axons.Translational vision science & technology · 2023Article
- Automated pipeline for nerve fiber selection and g-ratio calculation in optical microscopy: exploring staining protocol variations.Frontiers in neuroanatomy · 2023Article
- Protocol to image and analyze the morphology of mouse peripheral nerves using transmission electron microscopy.STAR protocols · 2022Article
- High-throughput segmentation of unmyelinated axons by deep learning.Scientific reports · 2022Article
- Histology-informed automatic parcellation of white matter tracts in the rat spinal cord.Frontiers in neuroanatomy · 2022Article
- Role of Dectin-1 in peripheral nerve injury.Frontiers in cellular neuroscience · 2022Article
- A shape-adjusted ellipse approach corrects for varied axonal dispersion angles and myelination in primate nerve roots.Scientific reports · 2021Article
- Tutorial: a computational framework for the design and optimization of peripheral neural interfaces.Nature protocols · 2020Review
- Dendritic Degeneration of Human Auditory Nerve Fibers and Its Impact on the Spiking Pattern Under Regular Conditions and During Cochlear Implant Stimulation.Frontiers in neuroscience · 2020Article
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Segmenting axon and myelin from microscopic images is relevant for studying the peripheral and central nervous system and for validating new MRI techniques that aim at quantifying tissue microstructure. While several software packages have been proposed, their interface is sometimes limited and/or they are designed to work with a specific modality (e.g., scanning electron microscopy (SEM) only). Here we introduce AxonSeg, which allows to perform automatic axon and myelin segmentation on histology images, and to extract relevant morphometric information, such as axon diameter distribution, axon density and the myelin g-ratio. AxonSeg includes a simple and intuitive MATLAB-based graphical user interface (GUI) and can easily be adapted to a variety of imaging modalities. The main steps of AxonSeg consist of: (i) image pre-processing; (ii) pre-segmentation of axons over a cropped image and discriminant analysis (DA) to select the best parameters based on axon shape and intensity information; (iii) automatic axon and myelin segmentation over the full image; and (iv) atlas-based statistics to extract morphometric information. Segmentation results from standard optical microscopy (OM), SEM and coherent anti-Stokes Raman scattering (CARS) microscopy are presented, along with validation against manual segmentations. Being fully-automatic after a quick manual intervention on a cropped image, we believe AxonSeg will be useful to researchers interested in large throughput histology. AxonSeg is open source and freely available at: https://github.com/neuropoly/axonseg.
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