NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects.
NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects.
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NODeJ：一个用于核对象3D分割的ImageJ插件。
DOI：
10.1186/s12859-022-04743-6
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发表时间：
2022-06-06
影响因子：
3
通讯作者：
Jacob, Yannick
中科院分区：
文献类型：
--
作者：
Dubos, Tristan;Poulet, Axel;Thomson, Geoffrey;Pery, Emilie;Chausse, Frederic;Tatout, Christophe;Desset, Sophie;van Wolfswinkel, Josien C.;Jacob, Yannick
染色质的三维核内排列会影响动植物系统中许多在DNA层面进行的细胞过程。染色质组织架构是一个动态过程，可能受到生物和非生物胁迫的影响。三维成像技术能够追踪这些动态变化，但目前仅有少数半自动处理方法可用于三维染色质组织架构的定量分析。
我们推出一种自动方法——核对象检测插件（Nuclear Object DetectionJ，简称NODeJ），它是作为ImageJ插件开发的。该程序可对三维图像中细胞核内的高强度区域进行分割与分析。NODeJ会对细胞核掩模执行拉普拉斯卷积，以增强核内物体的对比度，从而实现对它们的检测。我们重新分析了公开数据集，确定NODeJ能够准确识别用DAPI或Hoechst染色的拟南芥不同细胞核中的异染色质区域。NODeJ还能够检测DNA荧光原位杂交（FISH）实验中细胞核内的信号，从而得以分析特定的目标对象。
NODeJ通过避免半自动步骤，实现了对亚核结构的高效自动分析，减少了处理时间和分析偏差。NODeJ用Java编写，作为ImageJ插件提供，并带有命令行选项，以便进行更高通量的分析。NODeJ可从https://gitlab.com/axpoulet/image2danalysis/-/releases下载，源代码、文档及更多信息可在https://gitlab.com/axpoulet/image2danalysis获取。本研究中使用的图像可在https://www.brookes.ac.uk/indepth/images/ 和https://doi.org/10.15454/1HSOIE公开获取。
在线版本包含补充材料，网址为10.1186/s12859 - 022 - 04743 - 6。
The three-dimensional nuclear arrangement of chromatin impacts many cellular processes operating at the DNA level in animal and plant systems. Chromatin organization is a dynamic process that can be affected by biotic and abiotic stresses. Three-dimensional imaging technology allows to follow these dynamic changes, but only a few semi-automated processing methods currently exist for quantitative analysis of the 3D chromatin organization. We present an automated method, Nuclear Object DetectionJ (NODeJ), developed as an imageJ plugin. This program segments and analyzes high intensity domains in nuclei from 3D images. NODeJ performs a Laplacian convolution on the mask of a nucleus to enhance the contrast of intra-nuclear objects and allow their detection. We reanalyzed public datasets and determined that NODeJ is able to accurately identify heterochromatin domains from a diverse set of Arabidopsis thaliana nuclei stained with DAPI or Hoechst. NODeJ is also able to detect signals in nuclei from DNA FISH experiments, allowing for the analysis of specific targets of interest. NODeJ allows for efficient automated analysis of subnuclear structures by avoiding the semi-automated steps, resulting in reduced processing time and analytical bias. NODeJ is written in Java and provided as an ImageJ plugin with a command line option to perform more high-throughput analyses. NODeJ can be downloaded from https://gitlab.com/axpoulet/image2danalysis/-/releases with source code, documentation and further information avaliable at https://gitlab.com/axpoulet/image2danalysis. The images used in this study are publicly available at https://www.brookes.ac.uk/indepth/images/ and https://doi.org/10.15454/1HSOIE. The online version contains supplementary material available at 10.1186/s12859-022-04743-6.
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影响因子：
1.6
作者：
Skinner BM;Johnson EE
通讯作者：
Johnson EE
影响因子：
4.6
作者：
Arpòn J;Sakai K;Gaudin V;Andrey P
通讯作者：
Andrey P
影响因子：
5.3
作者：
Wang H;Dittmer TA;Richards EJ
通讯作者：
Richards EJ
影响因子：
64.8
作者：
通讯作者：
--
DOI：
10.1080/19491034.2020.1845012
发表时间：
2020-12
期刊：
Nucleus (Austin, Tex.)
影响因子：
--
作者：
Dubos T;Poulet A;Gonthier-Gueret C;Mougeot G;Vanrobays E;Li Y;Tutois S;Pery E;Chausse F;Probst AV;Tatout C;Desset S
通讯作者：
Desset S