基于DE-3D U-Net的斑马鱼后脑血管共聚焦显微图像分割和量化测量  

Segmentation and Quantification of Zebrafish Hindbrain Vessel Confocal Images Based on DE-3D U-Net

作　　者：郑文虎 李辉[2] 陈冲 王林波[2] ZHENG Wenhu;LI Hui;CHEN Chong;WANG Linbo(School of Biomedical Engineering,Division of Life Sciences and Medicine,University of Science and Technology of China,Hefei 230026,China;Jiangsu Key Laboratory of Medical Optics,Suzhou Institute of Biomedical Engineering and Technology,Chinese Academy of Sciences,Suzhou 215163,China)

机构地区：[1]中国科学技术大学生命科学与医学部生物医学工程学院,合肥230026 [2]中国科学院苏州生物医学工程技术研究所,苏州215163

出　　处：《激光生物学报》2024年第3期209-216,共8页Acta Laser Biology Sinica

基　　金：国家自然科学基金项目(62205368)。

摘　　要：斑马鱼后脑部位的脉络丛控制着大脑和血管之间的物质交换,脉络丛周围的血管异常可引发相关的脑血管疾病。本文首先对斑马鱼后脑部位的主要血管进行了连续成像,使用共聚焦显微镜拍摄正常情况和柱孢藻毒素处理后的斑马鱼胚胎,获得了斑马鱼在受精后43~63 h的系列三维图像。然后,进一步开发了图像分割的神经网络DE-3D U-Net用于主要后脑血管的分割。网络分割结果显示,3根主要血管的类别像素准确率分别为86.67%、93.18%和83.74%。最后,绘制了斑马鱼后脑血管发育曲线图。结果表明,3根主要的血管半径在高浓度的柱孢藻毒素处理后出现了18%左右的缩减,中脑静脉夹角出现了30°~50°的缩减。此研究提出了一个可用于斑马鱼后脑血管分割的神经网络模型,得出的数据可为斑马鱼脉络丛发育研究提供基础。The choroid plexues in the zebrafish hindbrain controls the exchange of substances between brain and its vessels,and the vascular abnormalities around the choroid plexues can lead to associated cerebrovascular diseases.We first performed serial imaging of the major blood vessels in the hindbrain region of zebrafish,and obtained a series of images of zebrafish between 43 hours and 63 hours after fertilization using confocal microscopy to photograph embryos under normal conditions and after cylindrospermopsin treatment.Afterwards,the DE-3D U-Net was developed for the segmentation of the hindbrain images.The segmentation results showed that the class pixel accuracy of DE-3D U-Net could reach to 86.67%,93.18%and 83.74%for the three main vessels and the segmentation results were used to plot vascularization curves.The quantitative results showed that the radii of the three vessels showed a reduction of 18%after treatment with high concentrations of cylindrospermopsin,and the angle of the mesencephalic vein showed a reduction of 30°to 50°.This study proposed a neural network for segmentation of hindbrain vessels of zebrafish,and it provided a basis for research on the development of zebrafish choroid plexsus.

关 键 词：斑马鱼 后脑血管 共聚焦显微成像 3D U-Net神经网络 柱孢藻毒素 

分 类 号：TP391[自动化与计算机技术—计算机应用技术]