Robust normalization protocols for multiplexed fluorescence bioimage analysis.
Robust normalization protocols for multiplexed fluorescence bioimage analysis.
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DOI：
10.1186/s13040-016-0088-2
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发表时间：
2016
期刊：
影响因子：
4.5
通讯作者：
Rajpoot NM
中科院分区：
文献类型：
--
作者：
Ahmed Raza SE;Langenkämper D;Sirinukunwattana K;Epstein D;Nattkemper TW;Rajpoot NM
在亚细胞水平上研究共定位蛋白的定位和相互作用对理解复杂的生物现象具有重要意义。最近绘制共定位蛋白的技术之一是使用循环方式的标准免疫荧光显微镜（Nat biotechnology 24:1270 - 8,2006; Proc Natl Acad Sci 110:11982 - 7,2013）。不幸的是，这些技术在一次跑步和不同跑步中受到蛋白质标记物信号强度和定位变化的影响。因此，在对数据进行进一步分析之前，有必要对多路生物成像（MBI）数据从多次运行到可比规模的预处理协议进行标准化。在本文中，我们比较了各种归一化方案，并在获得结果的基础上提出了一种鲁棒的归一化技术，该技术使用Toponome成像系统（TIS）对不同运行收集的MBI数据产生一致的结果。两名病理学家和两名生物学家对大肠癌患者样本TIS数据集的归一化结果进行了良好的评价。我们表明，在结直肠癌和组织学正常样本的细胞表型分布上，所提出的方法在Kullback-Leibler （KL）类之间产生较高的差异，在KL类之间产生较低的差异。本文的在线版本（doi:10.1186/s13040-016-0088-2）包含补充材料，仅供授权用户使用。
study of mapping and interaction of co-localized proteins at a sub-cellular level is important for understanding complex biological phenomena. One of the recent techniques to map co-localized proteins is to use the standard immuno-fluorescence microscopy in a cyclic manner (Nat Biotechnol 24:1270–8, 2006; Proc Natl Acad Sci 110:11982–7, 2013). Unfortunately, these techniques suffer from variability in intensity and positioning of signals from protein markers within a run and across different runs. Therefore, it is necessary to standardize protocols for preprocessing of the multiplexed bioimaging (MBI) data from multiple runs to a comparable scale before any further analysis can be performed on the data. In this paper, we compare various normalization protocols and propose on the basis of the obtained results, a robust normalization technique that produces consistent results on the MBI data collected from different runs using the Toponome Imaging System (TIS). Normalization results produced by the proposed method on a sample TIS data set for colorectal cancer patients were ranked favorably by two pathologists and two biologists. We show that the proposed method produces higher between class Kullback-Leibler (KL) divergence and lower within class KL divergence on a distribution of cell phenotypes from colorectal cancer and histologically normal samples. The online version of this article (doi:10.1186/s13040-016-0088-2) contains supplementary material, which is available to authorized users.
影响因子：
3
作者：
Loyek C;Rajpoot NM;Khan M;Nattkemper TW
通讯作者：
Nattkemper TW