Laboratoire Jean Perrin, UMR 8237 Sorbonne Universités, UPMC Université Paris, Paris, France.
Institute of Systems and Synthetic Biology, UMR 8030, CNRS, Commissariat à l'Energie Atomique et aux Energies Alternatives, Genopole, Université d'Evry Val-d'Essonne, Université Paris Saclay, Evry, France.
Nat Protoc. 2019 Nov;14(11):3144-3161. doi: 10.1038/s41596-019-0216-9. Epub 2019 Sep 25.
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 ~6 min on a regular computer. Numerous implemented algorithms, easy configuration and high modularity ensure wide applicability of the BACMMAN software.
在单细胞水平上分析细菌对于描述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）是一种软件，可快速可靠地自动化分析使用“母机”进行的高通量 2D 或 3D 时间序列图像，“母机”是一种非常流行的微流控设备，可用于在单细胞水平上研究细菌中的生物过程。在这里，我们描述了如何使用 BACMMAN 的一些功能，包括（i）细菌和细胞内荧光斑点的分割和跟踪，（ii）结果的可视化和编辑，（iii）为不同数据集配置图像处理管道，以及（iv）将 BACMMAN 与数据分析软件耦合，以可视化和分析具有特定属性的数据集子集。在专门用于分析母机数据的软件中，只有 BACMMAN 允许分割和跟踪细菌和细胞内斑点。对于一个位置、一个通道、1000 帧（2-GB 数据集），在普通计算机上进行图像处理大约需要 6 分钟。众多实现的算法、易于配置和高模块化确保了 BACMMAN 软件的广泛适用性。
