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基于 CNN 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.

机构信息

Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.

Institute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.

出版信息

PLoS One. 2020 Dec 8;15(12):e0243219. doi: 10.1371/journal.pone.0243219. eCollection 2020.


DOI:10.1371/journal.pone.0243219
PMID:33290432
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7723299/
Abstract

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.

摘要

在生物医学研究中,准确地对显微镜图像序列中的细胞进行分割和跟踪是一项重要任务,例如,用于研究组织、器官或整个生物体的发育。然而,在低信噪比的图像中分割粘连细胞仍然是一个具有挑战性的问题。在本文中,我们提出了一种用于分割显微镜图像中粘连细胞的方法。通过使用一种新的细胞边界表示方法,受距离图启发,我们的方法不仅能够利用粘连细胞,还能够在训练过程中利用接近的细胞。此外,这种表示方法对注释错误具有显著的鲁棒性,并且在分割训练数据中代表性不足或未包含的细胞类型的显微镜图像方面显示出有前景的结果。为了预测所提出的邻域距离,我们使用了具有两个解码器路径的自适应 U-Net 卷积神经网络 (CNN)。此外,我们还对基于图的细胞跟踪算法进行了适配,以在细胞跟踪任务上评估我们提出的方法。所提出的跟踪算法在代价函数中包括运动估计,以在短时间的帧序列中重新链接具有缺失分割掩模的跟踪。我们的基于检测的联合跟踪方法在 IEEE ISBI 2020 细胞跟踪挑战赛(http://celltrackingchallenge.net/)中证明了其潜力,我们的 KIT-Sch-GE 团队在多个数据集中使用单个分割模型获得了多个前三名的排名,包括两个最佳成绩。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/28962e5377af/pone.0243219.g013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/b2f6b1a1cc13/pone.0243219.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/3f52c7658639/pone.0243219.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/a45c42ed8b72/pone.0243219.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/5482eb7c49a7/pone.0243219.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/fec85e15e419/pone.0243219.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/d2300454fbcf/pone.0243219.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/0410bc7acd4d/pone.0243219.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/a88047d69dc9/pone.0243219.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/db0273803a9f/pone.0243219.g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/2da67b7e68b3/pone.0243219.g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/fc87f30c1853/pone.0243219.g011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/0f70315e8768/pone.0243219.g012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/28962e5377af/pone.0243219.g013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/b2f6b1a1cc13/pone.0243219.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/3f52c7658639/pone.0243219.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/a45c42ed8b72/pone.0243219.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/5482eb7c49a7/pone.0243219.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/fec85e15e419/pone.0243219.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/d2300454fbcf/pone.0243219.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/0410bc7acd4d/pone.0243219.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/a88047d69dc9/pone.0243219.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/db0273803a9f/pone.0243219.g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/2da67b7e68b3/pone.0243219.g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/fc87f30c1853/pone.0243219.g011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/0f70315e8768/pone.0243219.g012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b81d/7723299/28962e5377af/pone.0243219.g013.jpg

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本文引用的文献

[1]
nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer.

Cell Syst. 2020-5-20

[2]
Test-time augmentation for deep learning-based cell segmentation on microscopy images.

Sci Rep. 2020-3-19

[3]
Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl.

Nat Methods. 2019-10-21

[4]
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Med Image Anal. 2019-9-18

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Med Image Anal. 2019-10

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Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb.

Elife. 2018-3-29

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Nat Methods. 2017-12

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Cell Tracking Accuracy Measurement Based on Comparison of Acyclic Oriented Graphs.

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