Rachel ShekarThe Quantitative Plant website was developed to help researchers having to analyze plants to find the right image dataset, tool, or mathematical model for their research.
What was in 2013 solely a plant image analysis database has grown into a comprehensive database of public datasets for plant phenotyping, image analysis software tools and models for plants
Maintained by Guillaume Lobet and Clément Saint Cast, the Quantitative Plant website features 180 image software tools, 31 image datasets, and 101 plant and crop models as of March 2022.
Guillaume Lobet, an Assistant Professor in a joint position between the Forschungszentrum Jülich and the UCLouvain, is a plant enthusiast who is passionate about Open Science. I asked him why.
“Acquiring datasets is a long and (sometimes) expensive exercise. Publicly sharing a dataset can decrease its cost while at the same time increase its reproducibility and further use. Data repositories and the rise of data journals can even help get more citations. Reproducibility is critical, therefore not only data should be open, but software and mathematical model as well. Code repositories can prevent that academic software and tools perish after funding and incentives have run out. It provides more chances for long term maintenance through collaboration and can help with debugging the code and version control. Ultimately every step in the research process can be opened and the tools to do so are available” explains Guillaume Lobet.
How comprehensive is the Quantitative Plant website? If a tool is in the public sphere, it is manually curated by Guillaume Lobet and Clément Saint Cast. If something is missing, they welcome submissions.
The online database is not just a list of tools and mathematical models. Each is presented concisely in a consistent framework and is described by their general characteristics (e.g., plant part studied) and uses (e.g. species studied). They are referenced by one or more scientific articles presenting their characteristics or success stories.
This descriptive information allows users to query the database with keywords or browse it with pre-defined criteria such as the type of organ to analyze, the measurements to make, plant species, license type, and operating system.
“We believe public resource like this will provide a way to exchange and communicate about the development of new tools and models, but also facilitate collaboration and connection between the phenomics and modelling communities.”
For a comprehensive database of public datasets for plant phenotyping, see the Quantitative Plant website at https://www.quantitative-plant.org.
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