Image analysis

Phenomics Workshop at Purdue – be quick!

Purdue University’s Agronomy and Agricultural and Biological Engineering departments are offering a field-based Phenomics Workshop for crop research professionals involved in predicting yield and characterising biotic and abiotic stress, as well as engineers involved in developing and using sensors and sensor platforms for application.

Space is limited!

Date:  13 – 14 March 2017

Topics:  Prediction and Exploration of Agronomic Performance Using Integrated Data Sets • Effective Ground Truthing • Phenomics for Crop Improvement • Implementation of UAS Experiments • Image Analysis • Advanced Phenomic Analytical Techniques (i.e. reducing dimensionality, spatial statistics)

Cost:  $500 for professionals

Register here

For more information

Or contact Chad Martin – P: (765) 496­-3964   E:


Accurate field canopy temperature measured in seconds

A method for cost-effective, reliable and scalable airborne thermography has been developed, resolving a number of challenges surrounding accurate high-throughput phenotyping of canopy temperature (CT) in the field, such as weather changes and their influence on more time consuming measurement methods. Utilising a manned helicopter carrying a radiometrically-calibrated thermal camera, thermal image data is captured in seconds and processed within minutes using custom-developed software; an invaluable advantage for large forward genetic studies or plant breeding programs.

The method and research results, by a collaboration between CSIRO Agriculture and Food, the Australian Plant Phenomics Facility – High Resolution Plant Phenomics Centre, CSIRO Information Management and Technology, and the ARC Centre of Excellence for Translational Photosynthesis were published recently in Frontiers in Plant Science.

Read the full study“Methodology for high-throughput field phenotyping of canopy temperature using airborne thermography”, here or the abstract below.


Airborne thermography image acquisition and processing pipeline. Total time to acquire and process images for an experiment comprising 1,000 plots of size 2 x 6 m is ca. 25 min. (A) Image acquisition with helicopter. The images are recorded on a laptop and the passenger, left, provides real time assessment of the images and feedback to the pilot. This step takes < 10 s for an experiment comprising 1,000 plots of size 2 x 6 m. (B) Screenshot of custom-developed software called ChopIt. ChopIt is used for plot segmentation and extraction of CT from each individual plot for statistical analysis. This step takes ca. 20 min for an experiment comprising 1,000 plots of size 2 x 6 m.


Airborne thermography image acquisition system comprising a helicopter cargo pod with thermal camera and acquisition kit mounted on the skid of a Robinson R44 Ravel helicopter. Photo insert shows the inside of the helicopter cargo pod with arrow denoting FLR® SC645 thermal camera: ±2°C or ±2% of reading; < 0.05°C pixel sensitivity; 640×480 pixels; 0.7 kg without lens.


Lower canopy temperature (CT), resulting from increased stomatal conductance, has been associated with increased yield in wheat. Historically, CT has been measured with hand-held infrared thermometers. Using the hand-held CT method on large field trials is problematic, mostly because measurements are confounded by temporal weather changes during the time required to measure all plots. The hand-held CT method is laborious and yet the resulting heritability low, thereby reducing confidence in selection in large scale breeding endeavors. We have developed a reliable and scalable crop phenotyping method for assessing CT in large field experiments. The method involves airborne thermography from a manned helicopter using a radiometrically-calibrated thermal camera. Thermal image data is acquired from large experiments in the order of seconds, thereby enabling simultaneous measurement of CT on potentially 1000s of plots. Effects of temporal weather variation when phenotyping large experiments using hand-held infrared thermometers are therefore reduced. The method is designed for cost-effective and large-scale use by the non-technical user and includes custom-developed software for data processing to obtain CT data on a single-plot basis for analysis. Broad-sense heritability was routinely >0.50, and as high as 0.79, for airborne thermography CT measured near anthesis on a wheat experiment comprising 768 plots of size 2 × 6 m. Image analysis based on the frequency distribution of temperature pixels to remove the possible influence of background soil did not improve broad-sense heritability. Total image acquisition and processing time was ca. 25 min and required only one person (excluding the helicopter pilot). The results indicate the potential to phenotype CT on large populations in genetics studies or for selection within a plant breeding program.

Citation:  Deery DM, Rebetzke GJ, Jimenez-Berni JA, James RA, Condon AG, Bovill WD, Hutchinson P, Scarrow J, Davy R and Furbank RT (2016) Methodology for High-Throughput Field Phenotyping of Canopy Temperature Using Airborne Thermography. Front. Plant Sci. 7:1808. doi: 10.3389/fpls.2016.01808



Phenotyping takes to the skies

This year the Australian Plant Phenomics Facility (APPF) partnered with the Unmanned Research Aircraft Facility (URAF) at the University of Adelaide to provide improved phenotyping capabilities to support Australian plant and agricultural scientists.

The researchers use sensors on board remotely piloted aircraft to monitor plant growth and vigour for agricultural and ecological research. Platforms range from multi-copters to fixed wing aircraft, carrying cameras and multispectral and thermal sensors. Imagery captured produce GIS (geographic information system) layers used to integrate with field data to further develop relationships between plant growth, environmental conditions and plant treatment. The potential to measure parameters on field trials such as establishment, height, biomass, stress and nutritional status can be explored using this technology.

A recent episode on the youth science television show ‘Scope’ features the APPF field phenotyping capacity with Dr Ramesh Raja Segaran from the research team demonstrating the use of drones to investigate wheat tolerant of sodic soils. You can watch the episode here (the story commences at 16 min 19 sec)…


Dr Ramesh Raja Segaran demonstrating field phenotyping


Image-based phenotyping for non-destructive screening of different salinity tolerance traits in rice

Soil salinity is an abiotic stress wide spread in rice producing areas, limiting both plant growth and yield. The development of salt-tolerant rice requires efficient and high-throughput screening techniques to identify promising lines for salt affected areas. Advances made in image-based phenotyping techniques provide an opportunity to use non-destructive imaging to screen for salinity tolerance traits in a wide range of germplasm in a reliable, quantitative and efficient way. However, the application of image-based phenotyping in the development of salt-tolerant rice remains limited.

RiceJournalHairmansisA non-destructive image-based phenotyping protocol to assess salinity tolerance traits of two rice cultivars (IR64 and Fatmawati) has been established in this study. The response of rice to different levels of salt stress was quantified over time based on total shoot area and senescent shoot area, calculated from visible red-green-blue (RGB) and fluorescence images. The response of rice to salt stress (50, 75 and 100 mM NaCl) could be clearly distinguished from the control as indicated by the reduced increase of shoot area. The salt concentrations used had only a small effect on the growth of rice during the initial phase of stress, the shoot Na+ accumulation independent phase termed the ‘osmotic stress’ phase. However, after 20 d of treatment, the shoot area of salt stressed plants was reduced compared with non-stressed plants. This was accompanied by a significant increase in the concentration of Na+ in the shoot. Variation in the senescent area of the cultivars IR64 and Fatmawati in response to a high concentration of Na+ in the shoot indicates variation in tissue tolerance mechanisms between the cultivars.

Image analysis has the potential to be used for high-throughput screening procedures in the development of salt-tolerant rice. The ability of image analysis to discriminate between the different aspects of salt stress (shoot ion-independent stress and shoot ion dependent stress) makes it a useful tool for genetic and physiological studies to elucidate processes that contribute to salinity tolerance in rice. The technique has the potential for identifying the genetic basis of these mechanisms and assisting in pyramiding different tolerance mechanisms into breeding lines.


Aris Hairmansis, Bettina Berger, Mark Tester and Stuart John Roy (Corresponding author)
Rice 2014, 7:16 doi:10.1186/s12284-014-0016-3  Published: 14 August 2014