NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments
NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments
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DOI：
10.1093/bioinformatics/btq013
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发表时间：
2010-03-01
期刊：
影响因子：
5.8
通讯作者：
Boudier, T.
中科院分区：
文献类型：
--
作者：
Iannuccelli, E.;Mompart, F.;Boudier, T.
三维荧光原位杂交（3D-FISH）用于研究染色体或特定序列（如基因或RNA）在细胞核中的组织和定位。许多不同的程序（商业或免费）允许3D-FISH实验的图像分析。自动处理3D-FISH显微镜图像的更有效的开源程序之一是Smart 3D-FISH，这是一个ImageJ插件，旨在自动分析基因之间的距离。智能3D-FISH的缺点之一是它具有相当基本的用户界面，并以各种文本和图像文件产生结果，从而使数据后处理步骤耗时。我们开发了一个新的智能3D-FISH图形用户界面NEMO，它在同一个地方提供所有信息，以便可以有效地检查和验证结果。NEMO使用户能够在自动、半自动或手动检测模式下进行实验分析。我们还调整了Smart 3D-FISH，以更好地分析染色体区域。
Three-dimensional fluorescence in situ hybridization (3D-FISH) is used to study the organization and the positioning of chromosomes or specific sequences such as genes or RNA in cell nuclei. Many different programs (commercial or free) allow image analysis for 3D-FISH experiments. One of the more efficient open-source programs for automatically processing 3D-FISH microscopy images is Smart 3D-FISH, an ImageJ plug-in designed to automatically analyze distances between genes. One of the drawbacks of Smart 3D-FISH is that it has a rather basic user interface and produces its results in various text and image files thus making the data post-processing step time consuming. We developed a new Smart 3D-FISH graphical user interface, NEMO, which provides all information in the same place so that results can be checked and validated efficiently. NEMO gives users the ability to drive their experiments analysis in either automatic, semi-automatic or manual detection mode. We also tuned Smart 3D-FISH to better analyze chromosome territories.