注意神经细胞实例分割。

Attentive neural cell instance segmentation.

机构信息

Department of Computer Science, Rutgers University, Piscataway, NJ 08854, USA.

Lieber Institute for Brain Development, MD 21205, USA.

出版信息

Med Image Anal. 2019 Jul;55:228-240. doi: 10.1016/j.media.2019.05.004. Epub 2019 May 10.

Abstract

Neural cell instance segmentation, which aims at joint detection and segmentation of every neural cell in a microscopic image, is essential to many neuroscience applications. The challenge of this task involves cell adhesion, cell distortion, unclear cell contours, low-contrast cell protrusion structures, and background impurities. Consequently, current instance segmentation methods generally fall short of precision. In this paper, we propose an attentive instance segmentation method that accurately predicts the bounding box of each cell as well as its segmentation mask simultaneously. In particular, our method builds on a joint network that combines a single shot multi-box detector (SSD) and a U-net. Furthermore, we employ the attention mechanism in both detection and segmentation modules to focus the model on the useful features. The proposed method is validated on a dataset of neural cell microscopic images. Experimental results demonstrate that our approach can accurately detect and segment neural cell instances at a fast speed, comparing favorably with the state-of-the-art methods. Our code is released on GitHub. The link is https://github.com/yijingru/ANCIS-Pytorch.

摘要

神经细胞实例分割旨在联合检测和分割显微镜图像中的每个神经细胞,这对许多神经科学应用至关重要。该任务的挑战包括细胞黏附、细胞变形、细胞轮廓不清晰、低对比度的细胞突出结构以及背景杂质。因此,当前的实例分割方法通常精度不够。在本文中,我们提出了一种注意实例分割方法,该方法可以同时准确地预测每个细胞的边界框及其分割掩模。具体来说,我们的方法构建在一个联合网络上,该网络结合了单发多盒检测器(SSD)和 U-net。此外,我们在检测和分割模块中都使用了注意力机制,以使模型专注于有用的特征。我们在神经细胞显微镜图像数据集上验证了所提出的方法。实验结果表明,与最先进的方法相比,我们的方法可以快速准确地检测和分割神经细胞实例。我们的代码发布在 GitHub 上,链接是 https://github.com/yijingru/ANCIS-Pytorch。

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