Drs Bob Furbank and Xavier Sirault
Imaging technologies and extraction of quantitative data from images is a rapidly developing field in plant biology. Around 90% of human sensory input is visual, a major driver for the development of imaging techniques in biology and medicine, allowing skilled experts to extract both spatial and temporal information on the subject, whether it be a plant or a human patient.
For Plant Biology, imaging provides a non-invasive suite of tools to monitor plant responses to environment and explore the expression of the genome and the relationship between phenotype and genotype (Plant Phenomics, see https://www.plantphenomics.org.au/ ). What has sparked the rapid expansion of these technologies has been the technical revolution that allows image to be captured, manipulated and processed using sophisticated algorithms and high speed computing. Digital image processing is now becoming a common tool for biologists for analysing multi-dimensional dataset.
The capturing of image data and the processing of these images for extracting quantitative information are the foci of this section. Protocols in this section are designed to provide plant scientists with “how to” methods which facilitate data capture using imaging sensors as well as strategies for processing and interpreting these images.
The box above lists a subset of imaging technologies, from the macro to the micro scale, applied to Plant Biology. Relevant protocols are linked to each of these sections.
Note: These protocols were designed by plant biologists for plant biologists to help them carry out studies in the lab or in the field using these technologies.
Two-dimensional imaging techniques, i.e. visible imaging (or RGB), hyperspectral or multispectral imaging, thermal imaging, fluorescence imaging and radar imaging, are now common tools used by biologists to analyse plant growth, structure and function of root systems, leaves or whole plants, with possibilities of scaling up their usage to whole canopies and ecosystems – albeit difficult. These imaging systems allow spatio-temporal and non-destructive detection of photosynthesis, transpiration, stomatal response, water status, and chemical compounds in leaves. Image sequences, using any of these technologies, open a way to explore the kinematics and dynamics of these processes on an area or volume basis.
Protocols in the macro-imaging section are intended to cover issues related to optimal acquisition of images using these technologies, with either a two-dimensional or three-dimensional set-up, i.e. multiple-view reconstruction (i.e. visual hull), X-Ray computed tomography (CT), Magnetic Resonance Imaging (MRI) or Single Photon Emission Computed Tomography (SPECT).
Protocols for pre-processing, processing and analysing these complex data sets as well as combining various modalities (co-registration), e.g. combining fluorescence and thermal imaging (Omasa and Takayama 2003) are also intended for this section. (Not all the pages corresponding to the list below have been created as yet (see above box of Lower level sections). If you could like to contribute to writing any of the remainder, please Contact Us ).
Lower level sections
- 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
This part expands the macro-imaging technologies to the microscopic scale. Although, most of the protocols related to this sub-section are invasive, the similarities with the previous section in term of optimising acquisition or processing the resulting images justify its inclusion in this section “imaging technologies”.
Lower level sections
- Optical and Fluorescence microscopy
- Laser confocal scanning microscopy for semi-quantitative analysis
- Fourier transform infrared micro-spectroscopy for chemical composition and spatial distribution of metabolites in plant tissues
- Preparing samples for micro-imaging
- Image analysis
Omasa K and Takayama K (2003). Simultaneous measurement of stomatal conductance, non-photochemical quenching, and photochemical yield of photosystem II in intact leaves by thermal and chlorophyll fluorescence imaging. Plant & Cell Physiology 44: 1290-1300