BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies.
BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies.
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DOI：
10.1186/1471-2105-15-251
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发表时间：
2014-07-25
影响因子：
3
通讯作者：
Maglica Z
中科院分区：
文献类型：
--
作者：
Mekterović I;Mekterović D;Maglica Z
迄今为止，用于分析延时显微镜图像序列的软件仅适用于某些细菌和有限的条件。这些程序大多基于MATLAB，对于形状不规则、细胞分裂位点不清楚或生长在紧密堆积的小菌落中的微生物无效。不幸的是，许多感兴趣的生物体都具有这些特征，并且分析它们的图像序列仅限于耗时的手动处理。在这里，我们描述BactImAS -一个模块化的，多平台的，开源的，基于Java的软件，既作为一个独立的程序，也作为一个插件的冰。该软件旨在从细菌延时电影中提取和可视化定量数据。BactImAS使用半自动化方法，其中用户定义初始细胞，识别细胞分裂事件，并且在必要时，在用户友好的GUI和并入的ImageJ应用程序的帮助下手动校正细胞分割。该程序使用一种新开发的算法来分割和跟踪细胞，该算法是为具有难以分割的细胞的电影而设计的，这些细胞表现出帧与帧之间的小差异。以可配置的自动化方式从图像中提取测量值，并使用SQLite数据库存储，检索和交换所有采集的数据。最后，BactImAS可以生成可配置的谱系树可视化并将数据导出为CSV文件。我们在耻垢分枝杆菌的延时电影上测试了BactImAS，与手动分析相比，处理时间减少了至少10倍。我们通过在谱系树顶端显示icl表达和细胞生长的异质性来说明可视化工具的强大功能。该软件简化了整体延时电影的定量分析，是目前唯一可用的分枝杆菌样细胞分析软件。这将是感兴趣的社区的最终用户和开发人员的时间推移显微镜软件。本文的在线版本（doi：10.1186/1471-2105-15-251）包含补充材料，可供授权用户使用。
The software available to date for analyzing image sequences from time-lapse microscopy works only for certain bacteria and under limited conditions. These programs, mostly MATLAB-based, fail for microbes with irregular shape, indistinct cell division sites, or that grow in closely packed microcolonies. Unfortunately, many organisms of interest have these characteristics, and analyzing their image sequences has been limited to time consuming manual processing. Here we describe BactImAS – a modular, multi-platform, open-source, Java-based software delivered both as a standalone program and as a plugin for Icy. The software is designed for extracting and visualizing quantitative data from bacterial time-lapse movies. BactImAS uses a semi-automated approach where the user defines initial cells, identifies cell division events, and, if necessary, manually corrects cell segmentation with the help of user-friendly GUI and incorporated ImageJ application. The program segments and tracks cells using a newly-developed algorithm designed for movies with difficult-to-segment cells that exhibit small frame-to-frame differences. Measurements are extracted from images in a configurable, automated fashion and an SQLite database is used to store, retrieve, and exchange all acquired data. Finally, the BactImAS can generate configurable lineage tree visualizations and export data as CSV files. We tested BactImAS on time-lapse movies of Mycobacterium smegmatis and achieved at least 10-fold reduction of processing time compared to manual analysis. We illustrate the power of the visualization tool by showing heterogeneity of both icl expression and cell growth atop of a lineage tree. The presented software simplifies quantitative analysis of time-lapse movies overall and is currently the only available software for the analysis of mycobacteria-like cells. It will be of interest to the community of both end-users and developers of time-lapse microscopy software. The online version of this article (doi:10.1186/1471-2105-15-251) contains supplementary material, which is available to authorized users.
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影响因子：
4.5
作者：
Lo Scrudato M;Blokesch M
通讯作者：
Blokesch M
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影响因子：
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作者：
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通讯作者：
Ribeiro, Andre S.
影响因子：
82.9
作者：
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通讯作者：
McKinney, JD
影响因子：
48
作者：
de Chaumont, Fabrice;Dallongeville, Stephane;Olivo-Marin, Jean-Christophe
通讯作者：
Olivo-Marin, Jean-Christophe