FISH Finder: a high-throughput tool for analyzing FISH images
FISH Finder: a high-throughput tool for analyzing FISH images
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DOI：
10.1093/bioinformatics/btr053
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发表时间：
2011-04-01
期刊：
影响因子：
5.8
通讯作者：
Gilbert, David M.
中科院分区：
文献类型：
--
作者：
Shirley, James W.;Ty, Sereyvathana;Gilbert, David M.
动机：荧光原位杂交（FISH）用于研究细胞核内特定DNA序列的组织和定位。分析FISH图像的数据是一个繁琐的过程，会引起主观因素。自动FISH图像分析可以节省时间并获得客观数据分析的好处。虽然已经开发了几种FISH图像分析软件工具，但是它们通常使用基于阈值的分割算法来进行细胞核分割。由于荧光信号强度可以在实验之间、细胞之间以及在细胞内显著变化，因此基于阈值的分割是不灵活的并且通常不足以用于自动图像分析，从而导致额外的手动分割和潜在的主观偏差。为了克服这些问题，我们开发了一个名为FISH的图形软件工具，可以自动分析差异显着的FISH图像。通过将细胞核分割作为一个分类问题，采用复合贝叶斯分类器，以便利用上下文信息，从而实现可靠的分类和边界提取。这使得可以有效地和客观地分析FISH图像，而无需调整输入参数。此外，设计FISH探针以分析差异染色的FISH探针之间的距离。
Motivation: Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus. Analyzing the data from FISH images is a tedious process that invokes an element of subjectivity. Automated FISH image analysis offers savings in time as well as gaining the benefit of objective data analysis. While several FISH image analysis software tools have been developed, they often use a threshold- based segmentation algorithm for nucleus segmentation. As fluorescence signal intensities can vary significantly from experiment to experiment, from cell to cell, and within a cell, threshold- based segmentation is inflexible and often insufficient for automatic image analysis, leading to additional manual segmentation and potential subjective bias. To overcome these problems, we developed a graphical software tool called FISH Finder to automatically analyze FISH images that vary significantly. By posing the nucleus segmentation as a classification problem, compound Bayesian classifier is employed so that contextual information is utilized, resulting in reliable classification and boundary extraction. This makes it possible to analyze FISH images efficiently and objectively without adjustment of input parameters. Additionally, FISH Finder was designed to analyze the distances between differentially stained FISH probes.