ArticleCommunications biology2021
DeepACSON automated segmentation of white matter in 3D electron microscopy.
Article in Communications biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
- Dependence of the Extra-Cellular Diffusion Coefficient on the Fractions of Neurites and Cell Bodies in Gray Matter.Magnetic resonance in medicine · 2026Article
- BasNet: Attention U-Net-Based Automated Axon Segmentation in Bielschowsky Silver-Stained Histology.Neuroinformatics · 2026Article
- Axonal microstructure and compartmentalization impact the orientation and time dependence of mesoscopic transverse relaxation.Scientific reports · 2026Article
- Multimodal approach to characterize surgically removed epileptogenic zone from patients with focal drug-resistant epilepsy: From operating room to wet lab.Epilepsia open · 2026Article
- Advances in multiscale myelin imaging: from classical histology to functional insights.Frontiers in cellular neuroscience · 2026Review
- Validating the standard model of diffusion MRI in white matter with numerical substrates.Imaging neuroscience (Cambridge, Mass.) · 2026Article
- Data-driven classification of tissue water populations by massively multidimensional diffusion-relaxation correlation MRI.Frontiers in neuroscience · 2026Article
- Axon collateralization and focal myelin dystrophy alter action potential propagation in multicompartment pyramidal neuron models.PLoS computational biology · 2025Article
- Scattering approach to diffusion quantifies axonal damage in brain injury.Nature communications · 2025Article
- Article
- Quantifying axonal features of human superficial white matter from three-dimensional multibeam serial electron microscopy data assisted by deep learning.NeuroImage · 2025Article
- Predicting Mesoscopic Larmor Frequency Shifts in White Matter With Diffusion MRI-A Monte Carlo Study in Axonal Phantoms.NMR in biomedicine · 2025Article
- MRI-scale histology validates spatial sensitivity of in-vivo MRI-based axon radius estimation.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Large-scale EM data reveals myelinated axonal changes and altered connectivity in the corpus callosum of an autism mouse model.Frontiers in neuroinformatics · 2025Article
- Diffusion of brain metabolites highlights altered brain microstructure in type C hepatic encephalopathy: a 9.4 T preliminary study.Frontiers in neuroscience · 2024Article
- Article
- Volume electron microscopy in injured rat brain validates white matter microstructure metrics from diffusion MRI.Imaging neuroscience (Cambridge, Mass.) · 2024Article
- Exploring white matter dynamics and morphology through interactive numerical phantoms: the White Matter Generator.Frontiers in neuroinformatics · 2024Article
- A novel framework for in-vivo diffusion tensor distribution MRI of the human brain.NeuroImage · 2023Article
- White matter injury detection based on preterm infant cranial ultrasound images.Frontiers in pediatrics · 2023Article
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tracing the entirety of ultrastructures in large three-dimensional electron microscopy (3D-EM) images of the brain tissue requires automated segmentation techniques. Current segmentation techniques use deep convolutional neural networks (DCNNs) and rely on high-contrast cellular membranes and high-resolution EM volumes. On the other hand, segmenting low-resolution, large EM volumes requires methods to account for severe membrane discontinuities inescapable. Therefore, we developed DeepACSON, which performs DCNN-based semantic segmentation and shape-decomposition-based instance segmentation. DeepACSON instance segmentation uses the tubularity of myelinated axons and decomposes under-segmented myelinated axons into their constituent axons. We applied DeepACSON to ten EM volumes of rats after sham-operation or traumatic brain injury, segmenting hundreds of thousands of long-span myelinated axons, thousands of cell nuclei, and millions of mitochondria with excellent evaluation scores. DeepACSON quantified the morphology and spatial aspects of white matter ultrastructures, capturing nanoscopic morphological alterations five months after the injury.
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