用遗传算法精准追踪拟南芥根部细胞核，解决密集排列下的跟踪难题。
Accurate Tracking of Arabidopsis Root Cortex Cell Nuclei in 3D Time-Lapse Microscopy Images Based on Genetic Algorithm
- 基于遗传算法与细胞排列先验知识，分步实现粗到精的追踪。
- 在根尖长时间成像数据上实现高精度追踪，仅需少量人工修正。
- 适合植物发育研究者，尤其关注活体成像与细胞动态分析者。
拟南芥是研究植物生理与发育的重要模式植物。活体成像技术能可视化并量化植物发育中的基本过程。为揭示植物生长与细胞分裂的新机制，准确追踪活体图像中的细胞至关重要。现有常用软件TrackMate采用检测-追踪范式，使用Laplacian of Gaussian（LoG）进行斑点检测，结合线性分配问题（LAP）追踪器进行追踪，但在细胞密集排列时表现不佳。为此，本文提出一种基于遗传算法（GA）的精确追踪方法，融合拟南芥根部细胞排列规律与空间关系先验知识。方法采用由粗到精策略：先完成较简单的逐行细胞核追踪，再基于已知的细胞列线性排列及核间空间关系进行复杂追踪。该方法在拟南芥根尖长时间活体成像数据集上进行了评估，经少量人工校正后可实现高精度追踪。据我们所知，这是首次成功解决根茎分生组织时间序列显微镜中长期存在的细胞核追踪难题。
原文摘要 · Abstract (English)
Arabidopsis is a widely used model plant to gain basic knowledge on plant physiology and development. Live imaging is an important technique to visualize and quantify elemental processes in plant development. To uncover novel theories underlying plant growth and cell division, accurate cell tracking on live imaging is of utmost importance. The commonly used cell tracking software, TrackMate, adopts tracking-by-detection fashion, which applies Laplacian of Gaussian (LoG) for blob detection, and Linear Assignment Problem (LAP) tracker for tracking. However, they do not perform sufficiently when cells are densely arranged. To alleviate the problems mentioned above, we propose an accurate tracking method based on Genetic algorithm (GA) using knowledge of Arabidopsis root cellular patterns and spatial relationship among volumes. Our method can be described as a coarse-to-fine method, in which we first conducted relatively easy line-level tracking of cell nuclei, then performed complicated nuclear tracking based on known linear arrangement of cell files and their spatial relationship between nuclei. Our method has been evaluated on a long-time live imaging dataset of Arabidopsis root tips, and with minor manual rectification, it accurately tracks nuclei. To the best of our knowledge, this research represents the first successful attempt to address a long-standing problem in the field of time-lapse microscopy in the root meristem by proposing an accurate tracking method for Arabidopsis root nuclei.
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