FoCo: a simple and robust quantification algorithm of nuclear foci.
FoCo: a simple and robust quantification algorithm of nuclear foci.
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DOI：
10.1186/s12859-015-0816-5
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发表时间：
2015-11-21
影响因子：
3
通讯作者：
Schaber J
中科院分区：
文献类型：
--
作者：
Lapytsko A;Kollarovic G;Ivanova L;Studencka M;Schaber J
每个细胞核的γ H2 AX灶的数量是单个细胞中DNA双链断裂数量的公认量度。用于在培养细胞中检测γ H2 AX的实验技术之一是γ H2 AX和细胞核的免疫荧光标记，然后进行显微镜成像和分析。在这项研究中，我们提出了算法FoCo可靠和强大的自动核病灶计数单细胞图像。FoCo相对于其他软件包具有以下优点：i）能够可靠地量化甚至密集分布的病灶，例如，在受到高达10戈伊的辐射剂量的细胞的图像上，ii）在抑制离焦背景信号的意义上的焦点量化的鲁棒性，以及iii）其简单性。FoCo只需要5个参数，用户必须调整。FoCo是一个开源的用户友好的软件，具有用于单个病灶计数的GUI，即使对于低信噪比和密集分布的病灶，也能够产生可靠和稳健的病灶定量。本文的在线版本（doi：10.1186/s12859-015-0816-5）包含补充材料，可供授权用户使用。
The number of γH2AX foci per nucleus is an accepted measure of the number of DNA double-strand breaks in single cells. One of the experimental techniques for γH2AX detection in cultured cells is immunofluorescent labelling of γH2AX and nuclei followed by microscopy imaging and analysis. In this study, we present the algorithm FoCo for reliable and robust automatic nuclear foci counting in single cell images. FoCo has the following advantages with respect to other software packages: i) the ability to reliably quantify even densely distributed foci, e.g., on images of cells subjected to radiation doses up to 10 Gy, ii) robustness of foci quantification in the sense of suppressing out-of-focus background signal, and iii) its simplicity. FoCo requires only 5 parameters that have to be adjusted by the user. FoCo is an open-source user-friendly software with GUI for individual foci counting, which is able to produce reliable and robust foci quantifications even for low signal/noise ratios and densely distributed foci. The online version of this article (doi:10.1186/s12859-015-0816-5) contains supplementary material, which is available to authorized users.