CSIRO Agriculture and Food

Fertiliser start-up gets a boost at APPF

Plant Technologist

Resource Recovery Australia together with CSIRO, Cape York Partnership, Balkanu and Kalan Enterprises are developing new income streams for Cape York’s Aboriginal communities by producing organic soil-conditioners from an unlikely source, feral pigs, which cause vast environmental damage to native ecosystems.

A pilot project at the Australian Plant Phenomics Facility’s (APPF) Adelaide node, tested the effect of the ‘Feraliser’ at different concentrations on tomato growth.

“The data collected using the high-throughput phenotyping Smarthouse at the APPF provided valuable insights into the effectiveness of our product. We now know Feraliser performs just as well as the leading organic soil-conditioners currently on the market,” said Emmaline Froggatt from Resource Recovery Australia.

“Feraliser is very much at the start-up phase of development so costs are a big issue for us. The Australian Plant Phenomics Facility provided the information we needed without the expense of a full field trial.”

Find out more about Resource Recovery Australia.

To find out how the Australian Plant Phenomics Facility can support your research, go to our website or contact us.

Canberra, Camille and the Cropatron…

As the sun rises over another crisp autumn morning in Canberra, you will find French intern, Camille Mounier, keenly watching over her rice lines in the Cropatron at the Australian Plant Phenomics Facility’s node at CSIRO Agriculture and Food.

Her project, ‘A complex system biology approach to understand the factors affecting canopy photosynthesis’, is being led by Dr Xavier Sirault, Director of the node, in partnership with the Chinese Academy of Sciences.

The project team aim to develop system models of canopy photosynthesis for both rice and wheat, in particular, developing novel methods to combine these system models with phenomics data. This approach will help in the identification of the critical factors controlling photosynthetic energy conversion efficiency in C3 species with the view to improving canopy photosynthetic efficiency, and subsequently, crop yields in small grain cereals.

Using the Cropatron platform, Camille will acquire data on canopy growth, gas and energy exchange in order to validate the biophysical photosynthetic model developed by Prof Xinguang Zhu, Head of Plant Systems Biology Group at the CAS-MPG Partner Institute for Computational Biology.

The Cropatron is a PC2 compliant, fully environmentally controlled (temperature, CO2 and humidity) greenhouse equipped with an automated gantry system (operating at 3.5m above the floor) for proxy-sensing imaging of plants grown in mini canopies. The sensing head is composed of an hyperspectral camera (400-1000nm) for measuring chlorophyll pigments, Far IR imaging for proxy sensing of canopy conductance, LiDAR for quantifying canopy architecture and monitoring growth over time, lysimeters for measuring water use at plot level and a gas exchange chamber at canopy level for measuring canopy assimilation.

Academic and commercial plant scientists are welcome to access the Cropatron platform – find out about pricing, availability and bookings here.

 

Taking five with… Michael Schaefer

The three national nodes of the Australian Plant Phenomics Facility (APPF) are home to a highly talented team of plant science researchers and specialists. This passionate, cross-disciplinary team is skilled in areas such as agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics. But who are they?

Today we take five minutes to get to know…

Michael Schaefer, PhD

Tell us a little about where you work within the APPF.

I am based at the CSIRO node of the APPF in Canberra. This centre focuses on “deep phenotyping” (delving into metabolism and physiological processes within the plant) and “reverse phenomics” (dissecting traits to discover their mechanistic basis). Here, next generation research tools are being developed and applied to probe plant function and performance, under controlled conditions and in the field.

What do you do there?

I’m a Research Scientist and Team Leader of the Translational Phenomics and Services team. My team looks after all of the new projects that come into our node of the APPF, from dealing with clients directly, to designing experiments based on the client’s needs, right through to providing the final data products and support with analysis.

What is the best part of your job?

As one of the newest team members, the best part of my job has been meeting and working with new people and dealing with new projects in different plants and crops. Every case is different, so designing and running each project is unique which provides a lot of variety.

Where do you see plant phenomics research in 5-10 years time?

I think in 5-10 years’ time plant phenomics research will be very different. We can already see that sensors and technology are getting smaller, faster and cheaper. I think much of what we do with large sensors (lidar for example) will be replaced by much smaller handheld devices or drones that will process data on the fly and give you a result straight away. This will affect all areas of science, not just plant science, so I think it will just be something that we have to adjust to.

“The moment I realised I loved plant science was…”

Somewhere during my undergraduate degree. I was doing straight science, biology, chemistry and physics – very broad – and then I started making links with how physics could be related to the environment (i.e. plants etc.). This seemed to make more sense to me, as I could see the application and how it could directly affect people now, rather than working on something theoretical that may or may not ever be used.

If you could solve one plant science question, what would it be?

For me, I’m really interested in pastures, so it would be the holy grail to be able to accurately, remotely measure above-ground biomass and split it into the green and senesced fractions.

Pic of Michael Schaefer for blog

Michael Schaefer at the western entry of Angkor Wat, Cambodia

“When I am not working I am…”

At home spending time with my wife Ali and daughter Emilia, or outdoors playing cricket, golf or fishing.

If you could have one super power, what would it be?

Good question…. being able to bend time and space like Dr. Strange. That would be pretty cool!

“If I wasn’t a plant scientist I would be a…”

Fishing guide!

What is your most treasured possession?

They’re not a possession but my family are the most important to me.

If you could have dinner with two famous people who would they be?

Barack Obama and Tiger Woods.

What’s the one thing about you that would surprise people?

I have my private aeroplane pilot licence. I did my pilot training while I was doing my PhD – not that I get to fly much these days.

The APPF provides academic and commercial researchers with expert advice and access to high quality plant growth facilities and state-of-the-art automated phenotyping capabilities in controlled environments and in the field. We provide a suite of analytical tools to support high-throughput phenotyping and deep phenotyping in either controlled environments or in the field. Our dedicated team of experts provide consultation on project design and high quality customer support. If you would like to know more about our services and how we can support your plant science research, please contact us!

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.

field-canopy-temp-blog-image-2

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.

field-canopy-temp-blog-image-1

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.

Abstract

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