Tracking cells in Life Cell Imaging videos using topological alignments.
Tracking cells in Life Cell Imaging videos using topological alignments.
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DOI：
10.1186/1748-7188-4-10
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发表时间：
2009-07-16
期刊：
影响因子：
--
通讯作者：
Chen SS
中科院分区：
文献类型：
--
作者：
Mosig A;Jäger S;Wang C;Nath S;Ersoy I;Palaniappan KP;Chen SS
随着活细胞成像技术的日益普及，跟踪活细胞视频中的细胞和其他运动物体已经成为生物图像信息学的一大挑战。大多数细胞跟踪算法的固有问题是细胞分割过多或分割不足-许多算法倾向于将一个细胞识别为几个细胞，反之亦然。我们建议通过所谓的拓扑对齐来解决这个问题，我们将其应用于解决视频序列中两个连续帧的分段链接的问题。从传统分割过程的输出开始，我们通过将一帧中的片段集分配给下一帧中的片段集来对齐连续帧对。我们通过寻找两个线段层次之间的广义“二部匹配”的最大加权解来实现这一点，其中，我们从线段集的凸壳的相对重叠分数获得权重。对于匹配任务的求解，我们依赖于一个整数线性规划。实际实验表明，该方法能够有效地解决实际中的细胞匹配问题，对于大规模数字细胞分析系统(LSDCAS)数据集中的细胞跟踪是有效和有用的。该实现的源代码可从http://www.picb.ac.cn/patterns/Software/topaln.下载
With the increasing availability of live cell imaging technology, tracking cells and other moving objects in live cell videos has become a major challenge for bioimage informatics. An inherent problem for most cell tracking algorithms is over- or under-segmentation of cells – many algorithms tend to recognize one cell as several cells or vice versa. We propose to approach this problem through so-called topological alignments, which we apply to address the problem of linking segmentations of two consecutive frames in the video sequence. Starting from the output of a conventional segmentation procedure, we align pairs of consecutive frames through assigning sets of segments in one frame to sets of segments in the next frame. We achieve this through finding maximum weighted solutions to a generalized "bipartite matching" between two hierarchies of segments, where we derive weights from relative overlap scores of convex hulls of sets of segments. For solving the matching task, we rely on an integer linear program. Practical experiments demonstrate that the matching task can be solved efficiently in practice, and that our method is both effective and useful for tracking cells in data sets derived from a so-called Large Scale Digital Cell Analysis System (LSDCAS). The source code of the implementation is available for download from http://www.picb.ac.cn/patterns/Software/topaln.
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作者：
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