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Unlocking the potential of plant phenotyping data using PIPPA

Stijn Dhondt  
【摘要】:While digital phenotyping claimed his central role in many plant research projects,phenotypic data is being produced at high speed and at high quantity.High throughput phenotyping platforms continuously generate plant images with several modalities.Nowadays,the same system can acquire RGB,thermal infrared,fluorescence and hyperspectral images and stores both environmental and weighing and irrigation data.The next hurdle is to be able to properly manage the high amount of raw and derived data.At VIB we developed PIPPA as a central database and web interface with image and data visualization and analysis functionality.Several automated WIWAM phenotyping platforms,ranging from an XY table for controlled irrigation and imaging of Arabidopsis to a conveyor belt system for full life cycle analysis of maize plants,have been integrated with PIPPA.The interface allows scientists to setup and analyse their own experiments,while keeping all data together in a structured database.The database takes care of the data management and integration,linking images,metadata,environmental data,and image analysis and measurement results.As the software package is developed as a web interface,the tool is available on every computer within the department.Preprocessing of images,such as cropping,can be automated and image analysis is performed by starting a task on the server or computer cluster,for fast processing.The analysis framework is designed to support the integration of external image analysis scripts.Furthermore,environmental measurements,weighing and irrigation output,the experimental design,and image analysis results can all be graphically visualized within PIPPA,bringing the plant phenotyping results to your fingertips.Current and future developments focus on the interoperability of image processing tools and the public accessibility of raw phenotypic data to enable community based 'big data' analysis initiatives.
【作者单位】:Department of Plant Systems Biology,VIB,Technologiepark 927

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