Gebiss: an ImageJ plugin for the specification of ground truth and the performance evaluation of 3d segmentation algorithms
Gebiss: an ImageJ plugin for the specification of ground truth and the performance evaluation of 3d segmentation algorithms
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DOI：
10.1186/1471-2105-12-232
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发表时间：
2011-06-13
影响因子：
3
通讯作者：
Wasser, Martin
中科院分区：
文献类型：
--
作者：
Kriston-Vizi, Janos;Thong, Ng Wee;Wasser, Martin
背景：图像分割是定量显微镜检查中的关键步骤，有助于界定组织、细胞或亚细胞区室的区域。根据用户交互程度，分割方法可分为手动、自动或半自动方法。由于3D图像栈包含大量光学切片，通常需要自动方法。然而，某些应用从手动或半自动方法中获益。例如对信噪比差的3D图像进行定量，或者生成用于评估自动分割方法准确性的所谓的基准真值分割。
结果：我们开发了Gebiss，这是一个用于3D显微图像栈的交互式分割、可视化和定量的ImageJ插件。我们整合了多种现有的基于阈值分割和体积可视化的插件。
结论：我们展示了Gebiss在果蝇活胚胎细胞核分割以及果蝇幼虫脑神经退行性变定量中的应用。Gebiss是作为一个跨平台的ImageJ插件开发的，可在网络上免费获取，网址是http://imaging.bii.a - star.edu.sg/projects/gebiss/。
Background: Image segmentation is a crucial step in quantitative microscopy that helps to define regions of tissues, cells or subcellular compartments. Depending on the degree of user interactions, segmentation methods can be divided into manual, automated or semi-automated approaches. 3D image stacks usually require automated methods due to their large number of optical sections. However, certain applications benefit from manual or semi-automated approaches. Scenarios include the quantification of 3D images with poor signal-to-noise ratios or the generation of so-called ground truth segmentations that are used to evaluate the accuracy of automated segmentation methods.Results: We have developed Gebiss; an ImageJ plugin for the interactive segmentation, visualisation and quantification of 3D microscopic image stacks. We integrated a variety of existing plugins for threshold-based segmentation and volume visualisation.Conclusions: We demonstrate the application of Gebiss to the segmentation of nuclei in live Drosophila embryos and the quantification of neurodegeneration in Drosophila larval brains. Gebiss was developed as a cross-platform ImageJ plugin and is freely available on the web at http://imaging.bii.a-star.edu.sg/projects/gebiss/.