论文标题
使用基于CNN的距离预测和基于图的匹配策略的细胞分割和跟踪
Cell Segmentation and Tracking using CNN-Based Distance Predictions and a Graph-Based Matching Strategy
论文作者
论文摘要
显微镜图像序列中细胞的准确分割和跟踪是生物医学研究中的重要任务,例如研究组织,器官或整个生物的发展。但是,在低信噪比的图像中对接触细胞的分割仍然是一个具有挑战性的问题。在本文中,我们提出了一种在显微镜图像中分割接触细胞的方法。通过使用受距离图启发的细胞边界的新型表示,我们的方法不仅能够使用接触细胞,而且还可以在训练过程中关闭细胞。此外,这种表示对注释误差显着鲁棒,并显示出对训练数据中包含的显微镜图像分割的有希望的结果,这些显微镜图像不足或不包含的细胞类型。为了预测所提出的邻居距离,使用了带有两个解码器路径的适应的U-NET卷积神经网络(CNN)。此外,我们调整了基于图的单元格跟踪算法,以评估我们针对细胞跟踪任务的建议方法。改编的跟踪算法包括成本函数的运动估计,以重新链接轨道,并在短帧中缺少分段掩码。我们通过检测方法的组合跟踪已证明了其在IEEE ISBI 2020细胞跟踪挑战(http://celltrackingchallenge.net/)中的潜力,在这些挑战中,我们作为Kit-Sch-Sch-GE多个前三名排名,包括使用多元化数据集的单个分割模型,在其中作为Kit-SCH-SCH-GE多个前三名排名。
The accurate segmentation and tracking of cells in microscopy image sequences is an important task in biomedical research, e.g., for studying the development of tissues, organs or entire organisms. However, the segmentation of touching cells in images with a low signal-to-noise-ratio is still a challenging problem. In this paper, we present a method for the segmentation of touching cells in microscopy images. By using a novel representation of cell borders, inspired by distance maps, our method is capable to utilize not only touching cells but also close cells in the training process. Furthermore, this representation is notably robust to annotation errors and shows promising results for the segmentation of microscopy images containing in the training data underrepresented or not included cell types. For the prediction of the proposed neighbor distances, an adapted U-Net convolutional neural network (CNN) with two decoder paths is used. In addition, we adapt a graph-based cell tracking algorithm to evaluate our proposed method on the task of cell tracking. The adapted tracking algorithm includes a movement estimation in the cost function to re-link tracks with missing segmentation masks over a short sequence of frames. Our combined tracking by detection method has proven its potential in the IEEE ISBI 2020 Cell Tracking Challenge (http://celltrackingchallenge.net/) where we achieved as team KIT-Sch-GE multiple top three rankings including two top performances using a single segmentation model for the diverse data sets.