Deep convolutional neural networks for segmenting 3D in vivo multiphoton images of vasculature in Alzheimer disease mouse models
Deep convolutional neural networks for segmenting 3D in vivo multiphoton images of vasculature in Alzheimer disease mouse models
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DOI：
10.1371/journal.pone.0213539
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发表时间：
2019-03-13
期刊：
影响因子：
3.7
通讯作者：
Sabuncu, Mert R.
中科院分区：
文献类型：
--
作者：
Haft-Javaherian, Mohammad;Fang, Linjing;Sabuncu, Mert R.
组织的健康和功能依赖于其脉管系统网络来提供可靠的血液灌注。体积成像方法，如多光子显微镜，能够生成详细的血管3D图像，有助于我们了解血管结构在正常生理和疾病机制中的作用。血管的分割是一个核心的图像分析问题，是一个瓶颈，阻碍了系统地比较实验人群中的3D血管结构。我们探讨了使用卷积神经网络分割三维血管体积内的体内图像获得的多光子显微镜。我们在这个分割问题的背景下评估了不同的网络架构和机器学习技术。我们表明，我们优化的卷积神经网络架构具有自定义的损失函数，我们称之为DeepVess，产生了比最先进的方法更好的分割准确性，同时也比手动注释快了几个数量级。为了探索衰老和阿尔茨海默病对毛细血管的影响，我们将DeepVess应用于阿尔茨海默病的年轻和老年小鼠模型以及野生型同窝仔的皮质血管的3D图像。我们发现这些组之间毛细血管直径或迂曲度的分布几乎没有差异，但确实注意到在野生型和阿尔茨海默病小鼠模型中，与年轻动物相比，老年动物中较长毛细血管节段（>75 μ m）的数量减少。
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 (>75 mu m) in aged animals as compared to young, in both wild type and Alzheimer's disease mouse models.