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首页> 美国卫生研究院文献>G3: GenesGenomesGenetics >gitter: A Robust and Accurate Method for Quantification of Colony Sizes From Plate Images
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gitter: A Robust and Accurate Method for Quantification of Colony Sizes From Plate Images

机译：gitter：一种可靠准确的方法从板图像量化菌落大小。

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摘要

Colony-based screens that quantify the fitness of clonal populations on solid agar plates are perhaps the most important source of genome-scale functional information in microorganisms. The images of ordered arrays of mutants produced by such experiments can be difficult to process because of laboratory-specific plate features, morphed colonies, plate edges, noise, and other artifacts. Most of the tools developed to address this problem are optimized to handle a single setup and do not work out of the box in other settings. We present gitter, an image analysis tool for robust and accurate processing of images from colony-based screens. gitter works by first finding the grid of colonies from a preprocessed image and then locating the bounds of each colony separately. We show that gitter produces comparable colony sizes to other tools in simple cases but outperforms them by being able to handle a wider variety of screens and more accurately quantify colony sizes from difficult images. gitter is freely available as an R package from under the LGPL. Tutorials and demos can be found at
机译：基于菌落的筛选可量化固体琼脂平板上克隆种群的适合度，可能是微生物中基因组规模功能信息的最重要来源。由于实验室特有的板块特征，变形菌落，板块边缘，噪声和其他伪影，通过此类实验产生的突变体的有序阵列图像可能难以处理。为解决此问题而开发的大多数工具都经过优化，可以处理单个设置，并且在其他设置中无法立即使用。我们介绍了gitter，这是一种图像分析工具，用于对基于菌落的屏幕上的图像进行稳健而准确的处理。首先，从预处理图像中找到菌落的网格，然后分别定位每个菌落的边界。我们显示，在简单的情况下，gitter可产生与其他工具相当的菌落大小，但能够处理更多种屏幕并能更准确地从困难图像中量化菌落大小，从而胜过它们。 LGPL下的R包免费提供gitter。可以在以下位置找到教程和演示

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