CSIRO

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.

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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

 

 

Hello, ni hau, hola, guten tag, marhaba, bonjour… knowledge sharing the key to plant science success

The Australian Plant Phenomics Facility (APPF) is a national facility, available to all plant scientists, offering access to infrastructure that is not available at this scale or breadth in the public sectors anywhere else in the world.

Our three nodes in Adelaide and Canberra frequently welcome international research, industry and government guests to tour facilities and share knowledge in plant phenomics. Encouraging and supporting a global community focused on providing better nutrition and food security is key to the APPF vision we uphold.

Recently the CSIRO based HRPPC node of the APPF hosted a VIP visit by the Secretary of the Department of Industry, Innovation and Science, Glenys Beauchamp, CSIRO CEO, Larry Marshall, and the Canadian High Commissioner, His Excellency Paul Maddison.

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Larry Marshall (CEO, CSIRO), Glenys Beauchamp (Secretary, Department of Industry, Innovation and Science) and His Excellency Paul Maddison (Canadian High Commissioner) in front of a Phenomobile Lite at the APPF HRPPC           (Image courtesy of the CSIRO)

Hosted by Drs Xavier Sirault and Jose Jimenez-Berni, the visitors observed aspects of the work done by the APPF’s HRPPC in the controlled environment and had the opportunity to see first-hand one of the centre’s purpose built and designed Phenomobile Lite buggies which are used in the field for capturing plant traits.

The group discussed an overview of the range of research and development activities and issues facing Australia in science and technology and the Canadian High Commissioner shared his interested in areas of existing and potential collaboration between Australia and Canada.

We welcome and encourage engagement with the international plant science community. If you would like to visit one of our sites, discuss your plant phenomics research or book one of our facilities, please contact us – we love plant science!