data analysis

Taking five with Prof. Justin Borevitz

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…

Prof. Justin Borevitz

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Tell us about where you work within the APPF.

I lead the Canberra ANU node of the APPF. Our node is part of the Australian National University (ANU) Plant Science Division which is a world leader in plant research. In addition to the APPF, ANU Plant Sciences contains the Centre of Excellence (CoE) in Plant Energy Biology (PEB), CoE Translational Photosynthesis (CoETP) and the ANU-CSIRO Centre for Genomics, Metabolomics and Bioinformatics.

The Canberra ANU node of the APPF offers:

  • On-site phenomics and plant growth services – NextGen growth and phenotyping facilities for Australian and international researchers including greenhouses and growth chambers with timelapse imaging.
  • Genomics and bioinformatics, study design and data analysis support – analysis of phenotypic and genomics data and the opportunity to collaborate with world-class researchers in genomics, photosynthesis and bioinformatics.
  • Development and streamlining of cross-scale approaches in monitoring for scaling from lab to field, chamber to crop and forest.
  • Research and development of open source hardware and software pipelines and visualisation tools for enabling lower cost high-throughput phenotyping (HTP) and environmental monitoring.
  • A collaborative, cross-disciplinary approach to tackling the grand challenges associated with HTP and environmental monitoring.

We provide the only quarantine approved growth cabinets in Canberra for research purposes. A range of growth cabinets are available, capable of high resolution phenotyping of up to 2,000 small plants continuously in custom and climate-simulated growth environments (LED-based). Quantitative phenotypic screening for Arabidopsis and similar sized small plants can be conducted.

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Virtual reality is the new frontier in scientific visualisation. We also offer the ability to visualise a forest in virtual reality with sensor data overlays for a visually integrated understanding of the landscape. The APPF is a leader in the development of systems for visualising phenomics and environmental sensing data and point clouds in virtual and augmented reality (VR an AR). EcoVR is a virtual reality tool for recreating any forest or field site as a virtual space, where timelapse sensor and phenomics data can be overlaid on a 3-dimensional model of the landscape. VR and AR represent immense opportunities for revolutionising phenomics and education and for industry collaborations to develop new visualisation platforms for precision agriculture. These tools can help farmers understand their farming landscape and can be used by the forestry industry to understand how the landscape, environment and genetics interact to impact forest growth.

What do you do there?

I’m Scientific Director, overseeing all research projects.

What is the best part of your job?

I get the most enjoyment out of planning new experiments.

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

Digital, machine learning, interconnected sensors and farm equipment, and providing food and environmental services (carbon, water, nutrient management).

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

On my dad’s farm, growing new release strawberries when I was 15 years old.

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

Climate ready, high yielding crops that increase soil fertility.

“When I’m not working I am…”

You’ll find me kayaking or gardening (integrative problem solving).

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

I’d like to be able to communicate knowledge into understanding for rational decision making.

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

Definitely a ski bumb!

What is your idea of absolute happiness?

My family.

What is your most treasured possession?

Again, my family.

What scares you?

Cancer, but also reaching global limits.

If you could go backwards or forwards in time, where would you go?

I’d like to see my grandfather as a child in Poland on his family farm, and my daughter as a grandmother on her urban farm.

Contact Professor Justin Borevitz

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Supporting the agricultural industry through R&D to deliver successful new products to market

Developing and bringing new agricultural products to market can be costly and time consuming for industry. Nufarm Limited recently sought the technology and expertise of the Australian Plant Phenomics Facility (APPF) to provide independent testing on potential new foliar sprays under development.

“The full service approach at the APPF, from the technology to the specialist staff, really appealed to us”, said Chad Sayer from Nufarm’s Product Strategy Group.

“The non-destructive, high-throughput phenotyping technology at the APPF gave us the ability to gain insights into our products under development that we could not achieve anywhere else. Their highly skilled, specialist team helped us design our experiments and provided invaluable advice throughout the project, right through to the data analysis.

“This has been exciting for us. Our pilot project delivered such promising results, we already have a large project underway”.

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(L) Plants undergoing spray treatment.  (R) Daily observation and analysis by the horticultural team

“We have a bespoke approach, working closely with our customers to design their experiments to deliver the best results”, said Dr Bettina Berger, Scientific Director at the Adelaide node of the APPF.

Dr Berger and her colleagues provide consultation on all projects carried out at the Adelaide node, supporting the development of the initial design and execution of the research. The specialist horticultural team set up the experiments and manage them through to completion. Customers can make use of online monitoring and access of projects throughout the experiment stage via Zegami (‘live processing’ which allows result checking on a day-to-day basis). On completion of experiments image analysis and data analysis are handled by our skilled engineering, software and statistics team. The research team then provide consultation on results and further follow-up as required.

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Plants in a Smarthouse at the Adelaide node of the APPF undergo daily image analysis throughout the experiment

The APPF is available to all publicly or commercially funded researchers. For further information or to discuss how we can support your research, please visit the APPF website for contact details. For more information about this project, contact Dr Berger.

Nufarm Limited is an Australian company. It is one of the world’s leading crop protection and specialist seeds companies, producing products to help farmers protect their crops against damage caused by weeds, pests and disease. With operations based in Australia, New Zealand, Asia, Europe and the Americas, Nufarm sells products in more than 100 countries around the world. Find out more about Nufarm here.

Zegami is a web application which allows users to filter, sort and chart data from experiments undertaken in the Smarthouses at the APPF Adelaide node, with the unique feature of being able to group that data with the corresponding images. To get a real feel for the application, we highly recommend you watch the video. Further reading here.

Taking the kinks out of curves

In a recent paper, researchers have developed a methodology suitable for analyzing the growth curves of a large number of plants from multiple families. The corrected curves accurately account for the spatial and temporal variations among plants that are inherent to high-throughput experiments.

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An example of curve registration.  a The salinity sensitivity (SS) curves of the 16 functions from an arbitrary family, b SS curves after the curve registration, and c the corresponding time-warping functions. The salinity sensitivity on the y-axis of a and b refers to the derivative of the relative decrease in plant biomass

 

Advanced high-throughput technologies and equipment allow the collection of large and reliable data sets related to plant growth. These data sets allow us to explore salt tolerance in plants with sophisticated statistical tools.

As agricultural soils become more saline, analysis of salinity tolerance in plants is necessary for our understanding of plant growth and crop productivity under saline conditions. Generally, high salinity has a negative effect on plant growth, causing decreases in productivity.  The response of plants to soil salinity is dynamic, therefore requiring the analysis of growth over time to identify lines with beneficial traits.

In this paper the researchers, led by KAUST and including Dr Bettina Berger and Dr Chris Brien from the Australian Plant Phenomics Facility (APPF), use a functional data analysis approach to study the effects of salinity on growth patterns of barley grown in the high-throughput phenotyping platform at the APPF. The method presented is suitable to reduce the noise in large-scale data sets and thereby increases the precision with which salinity tolerance can be measured.

Read the full paper, “Growth curve registration for evaluating salinity tolerance in barley” (DOI: 10.1186/s13007-017-0165-7) here.

Find out how the Australian Plant Phenomics Facility can support your plant science research here.

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High-throughput phenotyping in the Smarthouse™ at the Adelaide node of the APPF

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Barley plants growing in the Smarthouse™

 

 

Last chance to secure an internship – apps close tomorrow!

This is your chance to investigate your plant science questions with the support of the highly skilled Australian Plant Phenomics Facility (APPF) team and the incredible technology and infrastructure we have available.

Internships are offered at the APPF in Adelaide and Canberra for enthusiastic, highly motivated postgraduate students with a real interest in our research and technology. Current postgraduate students in the following areas are encouraged to apply:

  • Agriculture
  • Bioinformatics
  • Biology
  • Biotechnology
  • Computer Science
  • Genetics
  • Mathematics
  • Plant physiology
  • Science
  • Software engineering
  • Statistics

Interstate students are strongly encouraged to apply!

We offer postgraduate internship grants which, in general, comprise:

  • $1,500 maximum towards accommodation in Adelaide or Canberra, if required
  • $500 maximum towards travel / airfare, if required
  • $10,000 maximum toward infrastructure use

The APPF has identified a number of priority research areas, each reflecting a global challenge and the role that advances in plant biology can play in providing a solution:

  • Tolerance to abiotic stress
  • Improving resource use efficiency in plants
  • Statistics and biometry
  • Application of mechatronic engineering to plant phenotyping
  • Application of image analysis techniques to understanding plant form and function

Students proposing other topics will also be considered.

APPF postgraduate internship grants involve access to the facility’s phenotyping capabilities to undertake collaborative projects and to work as an intern with the APPF team to learn about experimental design, image and data analysis in plant phenomics.

Selection is based on merit. Applications are assessed on the basis of academic record, research experience and appropriateness of the proposed research topic. Interviews may be conducted.

Postgraduate students are encouraged to contact APPF staff prior to submitting their application to discuss possible projects.

APPLICATIONS CLOSE:  31 March 2017. For further information click here.

 

Why apply for an internship with the APPF?

Well, aside from the fact we are a pretty nice bunch…

PhD student Rohan Riley, from Western Sydney University, undertook his research at APPF’s Adelaide node (The Plant Accelerator®) after being awarded a Postgraduate Student Internship Grant with us in 2015.

His research attempted to explain the unpredictability of plant growth responses in terms of resource limitation by introducing fungal communities to plants which are isolated from soils containing high or low levels of salinity and analysing the effects on plant stress at the phenotypic level.

This is what he had to say about his experience:

”Using daily phenotyping following the application of salt stress and controlled watering-to-weight in The Plant Accelerator® allowed for an unprecedented resolution and range of plant genetic changes in response to combinations of nutrient level, salinity and two different fungal communities that would not otherwise be achievable in a regular greenhouse,” said Rohan.

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”As a PhD student with limited experience in greenhouse experiments, the highly controlled growth conditions, large-scale automation, digital imaging and software technology (high-throughput phenotyping) at The Plant Accelerator® provided me with the work-space, expertise and technical support to make a complicated experiment possible.”

“It has been an amazing experience to conduct this experiment at The Plant Accelerator®. I am walking away from the facility with a big smile on my face, an incredible dataset for my PhD research and invaluable experience in greenhouse based plant research.”

To find out more about Rohan’s research:  https://www.researchgate.net/profile/Rohan_Riley

Exciting internship opportunity closing soon – apply now!

internships

The Australian Plant Phenomics Facility (APPF) is looking for enthusiastic, highly motivated postgraduate students with a real interest in our research and technology to join our team as interns. Current postgraduate students in the following areas are encouraged to apply:

  • Agriculture
  • Bioinformatics
  • Biology
  • Biotechnology
  • Computer Science
  • Genetics
  • Mathematics
  • Plant physiology
  • Science
  • Software engineering
  • Statistics

In order to attract the very best students, we offer postgraduate internship grants. In general, a grant is comprised of:

  • $1,500 maximum towards accommodation in Adelaide or Canberra, if required
  • $500 maximum towards travel / airfare, if required
  • $10,000 maximum toward infrastructure use

Interstate students are strongly encouraged to apply!

The APPF has identified a number of priority research areas, each reflecting a global challenge and the role that advances in plant biology can play in providing a solution:

  • Tolerance to abiotic stress
  • Improving resource use efficiency in plants
  • Statistics and biometry
  • Application of mechatronic engineering to plant phenotyping
  • Application of image analysis techniques to understanding plant form and function

Students proposing other topics will also be considered.

APPF postgraduate internship grants involve access to the facility’s phenotyping capabilities to undertake collaborative projects and to work as an intern with the APPF team to learn about experimental design, image and data analysis in plant phenomics.

Selection is based on merit. Applications are assessed on the basis of academic record, research experience and appropriateness of the proposed research topic. Interviews may be conducted.

APPLICATIONS CLOSE:  31 March 2017. For further information click here.

About us

The Australian Plant Phenomics Facility (APPF) underpins innovative plant phenomics studies to accelerate the development of new and improved crops, healthier food and more sustainable agricultural practice by providing researchers with access to high quality plant growth facilities and state-of-the-art automated phenotyping capabilities in controlled environments and in the field.

To help accelerate research outputs, our phenomics technologies are supported by experts from a number of fields, i.e. agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics.