ArticlePloS one2019
Deep convolutional neural networks for segmenting 3D in vivo multiphoton images of vasculature in Alzheimer disease mouse models.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 109 citations in OpenAlex.
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- A Three-dimensional Analytical Framework for Retinal Microvasculature Reveals Layer-associated Vulnerability in Development and Neovascular Remodeling.bioRxiv : the preprint server for biology · 2026Article
- Linking cross-species trajectories of cerebrovascular remodeling in aging and Alzheimer's disease to brain vessel transcriptome.bioRxiv : the preprint server for biology · 2026Article
- BVLab-analyzer: a unified visual toolbox for terabyte-scale whole-brain cell detection, neuron reconstruction, and vascular network extraction.Frontiers in neuroinformatics · 2026Article
- Longitudinal three-photon imaging for tracking amyloid plaques and vascular degeneration in a mouse model of Alzheimer's disease.Journal of biomedical optics · 2026Article
- Carbonic anhydrase inhibitors prevent presymptomatic capillary flow disturbances in a model of cerebral amyloidosis.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- A new dataset for measuring the performance of blood vessel segmentation methods under distribution shifts.PloS one · 2025Article
- Inhibiting CaNature neuroscience · 2024Article
- Unsupervised Segmentation of 3D Microvascular Photoacoustic Images Using Deep Generative Learning.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Vascularized organoid-on-a-chip: design, imaging, and analysis.Angiogenesis · 2024Review
- High-Spatiotemporal-Resolution Ultrasound Flow Imaging to Determine Cerebrovascular Hemodynamics in Alzheimer's Disease Mice Model.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- How is Big Data reshaping preclinical aging research?Lab animal · 2023Review
- Article
- High throughput detection of capillary stalling events with Bessel beam two-photon microscopy.Neurophotonics · 2023Article
- Digital labeling for 3D histology: segmenting blood vessels without a vascular contrast agent using deep learning.Biomedical optics express · 2023Article
- Toward next-generation endoscopes integrating biomimetic video systems, nonlinear optical microscopy, and deep learning.Biophysics reviews · 2023Review
- Near-lifespan longitudinal tracking of brain microvascular morphology, topology, and flow in male mice.Nature communications · 2023Article
- A dataset of rodent cerebrovasculature from in vivo multiphoton fluorescence microscopy imaging.Scientific data · 2023Article
- Multi-perspective label based deep learning framework for cerebral vasculature segmentation in whole-brain fluorescence images.Biomedical optics express · 2022Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
The health and function of tissue rely on its vasculature network to provide reliable blood perfusion. Volumetric imaging approaches, such as multiphoton microscopy, are able to generate detailed 3D images of blood vessels that could contribute to our understanding of the role of vascular structure in normal physiology and in disease mechanisms. The segmentation of vessels, a core image analysis problem, is a bottleneck that has prevented the systematic comparison of 3D vascular architecture across experimental populations. We explored the use of convolutional neural networks to segment 3D vessels within volumetric in vivo images acquired by multiphoton microscopy. We evaluated different network architectures and machine learning techniques in the context of this segmentation problem. We show that our optimized convolutional neural network architecture with a customized loss function, which we call DeepVess, yielded a segmentation accuracy that was better than state-of-the-art methods, while also being orders of magnitude faster than the manual annotation. To explore the effects of aging and Alzheimer's disease on capillaries, we applied DeepVess to 3D images of cortical blood vessels in young and old mouse models of Alzheimer's disease and wild type littermates. We found little difference in the distribution of capillary diameter or tortuosity between these groups, but did note a decrease in the number of longer capillary segments (>75μm) in aged animals as compared to young, in both wild type and Alzheimer's disease mouse models.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.