Plant image analysis is a crucial step in the phenotypic characterization of complex plants' physiological traits while working with large and demanding datasets. Here we present a collection of open source applications that can be scaled up

Plant phenotypic analysis software is a critical component of a Plant Phenotyping Research Toolbox (PPRT), a set of tools for the analysis of plant phenotypes in the context of a particular research project that relies on imaging. Currently, there are many software packages that provide both plant analysis and phenomics data analysis capabilities, but either they are behind a costly paywall or have limited functionalities. However, the number of available packages and the types of datasets that are available have greatly increased over the years.

Here we will provide an overview of some of these software tools and their functions, including an introduction to how data can be organized and analyzed using either regular macro imaging tools such a SRL cameras, to more specialized microscopy imaging.


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David Jaime Castilloabout 2 months ago

Further tools can be also found here: https://www.guillaumelobet.be/tools

Keith Loritzabout 1 month ago

WOW! Thanks David for the all inclusive listing. Was this a lifetimes worth of compiling or a VERY large group effort?

David Jaime Castilloabout 1 month ago

Hi Keith, In my understanding the Lobet group is working with several other universities, and the apps have been growing in number and implementations. As you can see a minor number are under a paid wall, the rest have been developed by independent groups. I'm reviewing other repositories with similar applications but many have referred to Guillaume's work as the main drive curating the database. I promise to upload any updates or similar efforts. Cheers! ;)

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