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叶形分析工具:LAMINA a tool for rapid quantification of leaf size and shape parameters  

2012-08-06 11:30:04|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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Background

An increased understanding of leaf area development is important in a number of fields: in food and non-food crops, for example short rotation forestry as a biofuels feedstock, leaf area is intricately linked to biomass productivity; in paleontology leaf shape characteristics are used to reconstruct paleoclimate history. Such fields require measurement of large collections of leaves, with resulting conclusions being highly influenced by the accuracy of the phenotypic measurement process.

Results

We have developed LAMINA (Leaf shApe deterMINAtion), a new tool for the automated analysis of images of leaves. LAMINA has been designed to provide classical indicators of leaf shape (blade dimensions) and size (area), which are typically required for correlation analysis to biomass productivity, as well as measures that indicate asymmetry in leaf shape, leaf serration traits, and measures of herbivory damage (missing leaf area). In order to allow Principal Component Analysis (PCA) to be performed, the location of a chosen number of equally spaced boundary coordinates can optionally be returned.

Conclusion

We demonstrate the use of the software on a set of 500 scanned images, each containing multiple leaves, collected from a common garden experiment containing 116 clones of Populus tremula (European trembling aspen) that are being used for association mapping, as well as examples of leaves from other species. We show that the software provides an efficient and accurate means of analysing leaf area in large datasets in an automated or semi-automated work flow.

Author information ? Article notes ? Copyright and License information ?

Availability and requirements

Project name: LAMINA: Leaf shApe deterMINAtion

Project home page: http://sourceforge.net/projects/lamina

Operating system(s): Platform independent

Programming language: Java

Other requirements: Java 1.4.x or higher. LAMINA uses the Java Advanced Imaging (JAI) package http://java.sun.com/javase/technologies/desktop/media/jai/ to support common image file formats, which is bundled with the installation and hence no additional installation should be required.

License: GNU GPL2


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