High-throughput detection and tracking of cells and intracellular spots in mother machine experiments
High-throughput detection and tracking of cells and intracellular spots in mother machine experiments
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DOI：
10.1038/s41596-019-0216-9
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发表时间：
2019-11-01
期刊：
影响因子：
14.8
通讯作者：
Robert, Lydia
中科院分区：
文献类型：
--
作者：
Ollion, Jean;Elez, Marina;Robert, Lydia
单细胞水平的细菌分析对于表征细胞异质性发挥重要作用的过程至关重要。 BACMMAN（细菌母机分析）是一款软件，允许对来自使用“母机”实验的高通量 2D 或 3D 时间序列图像进行快速、可靠的自动图像分析，“母机”是一种非常流行的微流体设备，允许在单细胞水平上研究细菌中的生物过程。在这里，我们描述如何使用一些 BACMMAN 功能，包括 (i) 细菌和细胞内荧光点的分割和跟踪，(ii) 结果的可视化和编辑，(iii) 配置(iv) BACMMAN 与数据分析软件耦合，用于对具有特定属性的数据子集进行可视化和分析。在专门用于分析母机数据的软件中，只有 BACMMAN 可以对细菌和细胞内斑点进行分割和跟踪。对于具有 1,000 帧（2 GB 数据集）的单位置、单通道，图像处理时间与普通计算机上的 6 分钟类似。众多的实施算法、简单的配置和高度模块化确保了 BACMMAN 软件的广泛适用性。
The analysis of bacteria at the single-cell level is essential to characterization of processes in which cellular heterogeneity plays an important role. BACMMAN (bacteria mother machine analysis) is a software allowing fast and reliable automated image analysis of high-throughput 2D or 3D time-series images from experiments using the 'mother machine', a very popular microfluidic device allowing biological processes in bacteria to be investigated at the single-cell level, Here, we describe how to use some of the BACMMAN features, including (i) segmentation and tracking of bacteria and intracellular fluorescent spots, (ii) visualization and editing of the results, (iii) configuration of the image-processing pipeline for different datasets and (iv) BACMMAN coupling to data analysis software for visualization and analysis of data subsets with specific properties. Among software specifically dedicated to the analysis of mother machine data, only BACMMAN allows segmentation and tracking of both bacteria and intracellular spots. For a single position, single channel with 1,000 frames (2-GB dataset), image processing takes similar to 6 min on a regular computer. Numerous implemented algorithms, easy configuration and high modularity ensure wide applicability of the BACMMAN software.