Automated 3D bio-imaging analysis of nuclear organization by NucleusJ 2.0.
Automated 3D bio-imaging analysis of nuclear organization by NucleusJ 2.0.
复制标题
DOI：
10.1080/19491034.2020.1845012
复制
发表时间：
2020-12
期刊：
影响因子：
--
通讯作者：
Desset S
中科院分区：
文献类型：
--
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
NucleusJ 1.0是一个ImageJ插件，是分析动植物细胞中核形态和染色质组织的有用工具。NucleusJ 2.0是NucleusJ的新版本，其中使用命令行用户界面可以更快地实现图像处理。从大的3D核集合开始，可以通过先前开发的Otsu修改的方法或通过新的3D礼物包裹方法来执行分割，从而更好地考虑到核凹陷和未染色的核仁。通过使用https://www.brookes.ac.uk/indepth/images/.社区可用的三种类型的数据集，对这两种互补方法的准确性进行了比较最后，使用原始的植物遗传物质，通过评估其对DNA染料染色的细胞核或3D-DNA荧光原位杂交后的核的效率来评估NucleusJ 2.0。有了这些改进，NucleusJ 2.0允许生成用户管理的大型数据集，这些数据集将对软件基准测试或训练卷积神经网络有用。
NucleusJ 1.0, an ImageJ plugin, is a useful tool to analyze nuclear morphology and chromatin organization in plant and animal cells. NucleusJ 2.0 is a new release of NucleusJ, in which image processing is achieved more quickly using a command-lineuser interface. Starting with large collection of 3D nuclei, segmentation can be performed by the previously developed Otsu-modified method or by a new 3D gift-wrapping method, taking better account of nuclear indentations and unstained nucleoli. These two complementary methods are compared for their accuracy by using three types of datasets available to the community at https://www.brookes.ac.uk/indepth/images/. Finally, NucleusJ 2.0 was evaluated using original plant genetic material by assessing its efficiency on nuclei stained with DNA dyes or after 3D-DNA Fluorescence in situ hybridization. With these improvements, NucleusJ 2.0 permits the generation of large user-curated datasets that will be useful for software benchmarking or to train convolution neural networks.
登录
查看更多内容
影响因子：
9.4
作者：
Benoit, Matthias;Simon, Lauriane;Probst, Aline V.
通讯作者：
Probst, Aline V.
影响因子：
7.2
作者：
BAUWENS, S;KATSANIS, K;ENGLER, G
通讯作者：
ENGLER, G
影响因子：
5.8
作者：
Le, Sebastien;Josse, Julie;Husson, Francois
通讯作者：
Husson, Francois
影响因子：
3.3
作者：
Chytilova, E;Macas, J;Galbraith, DW
通讯作者：
Galbraith, DW
影响因子：
6.9
作者：
Graumann, Katja;Vanrobays, Emmanuel;Tatout, Christophe
通讯作者：
Tatout, Christophe