MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis.
MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis.
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DOI：
10.1038/nmicrobiol.2016.77
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发表时间：
2016-06-20
影响因子：
28.3
通讯作者：
Brun, Yves V.
中科院分区：
文献类型：
--
作者：
Ducret, Adrien;Quardokus, Ellen M.;Brun, Yves V.
细菌和亚细胞蛋白定位动力学的单细胞分析表明，细菌具有复杂的生命周期，细胞骨架蛋白网络，和复杂的信号转导途径驱动的本地化蛋白。在这种实验中产生的多维图像的体积和检测、关联和跟踪细胞和亚细胞特征所需的计算时间构成了相当大的挑战，特别是对于高通量实验。因此，需要一种通用的、计算上高效的图像分析工具，其能够以有意义且无偏见的方式从图像中提取期望的关系。在这里，我们介绍MicrobeJ，一个开源平台ImageJ的插件。MicrobeJ提供了一个全面的框架来处理来自各种显微镜实验的图像，特别强调大型图像集。它执行最常见的强度和形态测量以及极点，隔膜，荧光灶和细胞器的定制检测，以亚像素分辨率确定它们的亚细胞定位，并随时间跟踪它们。由于图像、测量值和所有来自它们的数据表示之间保持着动态链接，因此编辑器和高级数据表示工具套件有助于图像分析过程，并提供了一种可靠的方法来验证数据的准确性和真实性。
Single cell analysis of bacteria and subcellular protein localization dynamics has shown that bacteria have elaborate life cycles, cytoskeletal protein networks, and complex signal transduction pathways driven by localized proteins. The volume of multi-dimensional images generated in such experiments and the computation time required to detect, associate, and track cells and subcellular features pose considerable challenges, especially for high-throughput experiments. Therefore, there is a need for a versatile, computationally efficient image analysis tool capable of extracting the desired relationships from images in a meaningful and unbiased way. Here we present MicrobeJ, a plug-in for the open-source platform ImageJ. MicrobeJ provides a comprehensive framework to process images derived from a wide variety of microscopy experiments with special emphasis on large image sets. It performs the most common intensity and morphology measurements as well as customized detection of poles, septa, fluorescent foci, and organelles, determines their sub-cellular localization with sub-pixel resolution, and tracks them over time. Because a dynamic link is maintained between the images, measurements, and all data representations derived from them, the editor and suite of advanced data presentation tools facilitates the image analysis process and provides a robust way to verify the accuracy and veracity of the data.
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细菌形态发生和细胞内时空动力学的高通量，子像素精确分析。
影响因子：
3.6
作者：
Sliusarenko O;Heinritz J;Emonet T;Jacobs-Wagner C
通讯作者：
Jacobs-Wagner C
影响因子：
2.1
作者：
KIM, MK;HARWOOD, CS
通讯作者：
HARWOOD, CS
影响因子：
48
作者：
de Chaumont, Fabrice;Dallongeville, Stephane;Olivo-Marin, Jean-Christophe
通讯作者：
Olivo-Marin, Jean-Christophe
影响因子：
5.2
作者：
Vischer NO;Verheul J;Postma M;van den Berg van Saparoea B;Galli E;Natale P;Gerdes K;Luirink J;Vollmer W;Vicente M;den Blaauwen T
通讯作者：
den Blaauwen T
影响因子：
3
作者：
Mekterović I;Mekterović D;Maglica Z
通讯作者：
Maglica Z