Robert Furbank


This section is intended for protocols relating to the following areas, some of which are described in more detail below:

  • Digital imaging-based growth analysis and high throughput analysis
  • Shape analysis and vector analysis for studying growth and development
  • Hyperspectral imaging for leaf and canopy level environmental response
  • Near-infrared imaging for tissue water content
  • Fluorescence imaging of photosynthetic performance
  • X-ray computed tomography for root and shoot architecture in vivo
  • Magnetic Resonance imaging and isotopic PET scanning: exploring dynamic processes
  • Far infrared imaging for canopy and leaf temperature determination
  • Terahertz imaging of plant function
  • Ground penetrating radar and electrical resistance tomography for imaging soil properties
  • Image analysis

Digital imaging based growth analysis

Conventional analysis of plant growth over time requires laborious destructive analysis of replicated individual plants. Such methods have shortcomings such as the inability to follow a single individual over its lifecycle and due to the labour intensive measurements and space requirements for plant culture, it is difficult to examine growth dynamics with fine temporal resolution. Digital imaging using conventional digital cameras or sophisticated multispectral systems avoid these problems and can be used to generate plant area or volume over time. This section is intended for protocols which describe how to acquire imaging data in 2-D and pseudo-3D from 2-D views, as well as analysis of such data. For a more detailed summary, see Imaging-based plant growth analysis.

3-D modelling of plants

Capture of images of plants from multiple viewing angles allows the reconstruction of a 3-D model, using appropriate software to convert 2-D silhouettes to a 3-D volume. Protocols for acquiring these data and analysing the 3-D models produced in silico are described.

Chlorophyll Fluorescence Imaging

Fluorescence from the chlorophyll molecules in the light harvesting complexes of chloroplasts accounts for less than 1% of the energy balance of a leaf yet by measuring this fluorescence and de-convolution of the fluorescence quenching parameters a sensitive method of calculating electron transport rate and photodamage and photoprotection parameters is provided. If a suitable camera system is used, fluorescence by photosynthetic structures can be monitored on a pixel by pixel basis, giving spatial information and facilitating high throughput measurements of many plants in trays. Methods for capturing these data by pulse amplitude modulate fluorescence imaging are described and protocols for deriving quenching coefficients and useful fluorescence parameters described and the challenges and inaccuracies discussed.

X-ray CT, MRI and isotopic PET scanning for root and shoot architecture and function in vivo

Digital imaging of shoots and roots to obtain area, volume and structure is confounded by “occlusions”; ie in the case of shoots, by overlapping leaves and other biomass and in the case of roots, by the soil substrate. These problems can be overcome to some degree by using high energy radiation rather than light as the probe. In the case of X-ray CT resolution in the micrometer range can be obtained by micro CT while MRI and PET scanning can be also be used for dynamic information on flux of solutes and isotopes. As these tools are very specialised and requiring expensive equipment, the applications and the short comings of the techniques rather than the protocols are presented. For a specific summary, see Imaging of radionuclides.

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