Image-based phenotyping

The Centre for Plant Integrative Biology (CPIB) has worked closely with experts from Nottingham, Jülich, Montpellier and Louvain to develop an XML-based file format, Root System Markup Language, which has been adopted by developers of root phenotyping systems. CyVerse UK’s image-based phenotyping applications will build on the development of RSML, encouraging further sharing and interoperability between phenotyping tools. The tool set will include:

  • RootTrace: Growth Analysis of Seedlings: With a fixed or controllable camera, RootTrace recovers seedling growth, curvature and branching number from plant root images captured against any distinctive background. From an image sequence and set of points marked on the first image, RootTrace generates a 2D heat-map visualisation of seedling growth and curvature and a symbolic description of the visible root system architectures.
  • RootNav: Recovering 2D Root Systems Architectures of Crop Plants: Extends the techniques underlying RootTrace to more complex root architectures. Images are again obtained with standard colour cameras, but capture larger growth surfaces supporting older roots. RootNav provides a structural description of the root, from which a wide variety of traits can be computed; expressed in the internationally agreed standard format, RSML.
  • RooTrak: Recovering 3D Root Systems Architectures of Plants Grown in Soil: Based on visual tracking techniques, RooTrak is capable of segmenting single/multiple root system architectures from the solid environment in x-ray CT images of soil-grown plants. It is anticipated that access to the UK iPlant compute power will reduce processing times.
  • RSML Root Viewer: Viewing Root System Architectures: A root system viewer allowing users to visualise and extract traits of interest from RSML format files. This enables them to compare and contrast results obtained with each of the tools described above, and examine different ways of summarising those descriptions to uncover key root traits.