Contact 2017-12-12T15:44:32+00:00

Contact Us

The Australian Plant Phenomics Facility (APPF) is strategically located at three renowned plant research organisations in Australia, enabling us to benefit from a world class concentration of expertise in plant and soil science. You will find our facilities at the University of Adelaide in South Australia, and the Australian National University and CSIRO Agriculture and Food in Canberra.

Adelaide
Canberra (CSIRO)
Canberra (ANU)
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Adelaide

The Plant Accelerator® at the University of Adelaide

A central component of The Plant Accelerator® (TPA) is the first automated high-throughput phenotyping system in Australia, which remains unique in both scale and open-access policy, attracting researchers from Australia and overseas. The system boasts a range of imaging technologies (RGB, infrared, fluorescence and hyperspectral imaging) to facilitate innovative high-quality research into plant performance in different environments.

Researchers from the public and private sector benefit from the expertise in design, management, operation and analysis of large scale phenotyping experiments offered by TPA, which has resulted in many high-impact publications. The facility’s phenotyping capacity has expanded in recent years to incorporate DroughtSpotter platforms to support precision heat and drought screenings and field phenotyping services, offered in partnership with the Unmanned Research Aircraft Facility (URAF) at the University of Adelaide. Plans to offer aerial phenotyping via Airborne Research Australia (ARA) and ground-based phenotyping are being developed with input from potential users to align with grant applications.

TPA is located at the University of Adelaide’s renowned Waite Research Precinct, the largest agricultural research, education and commercialisation precinct in the Southern Hemisphere. Established in 1924, ‘The Waite’ is a co-located partnership of 15 complementary organisations and centres engaged in world-class research and development in plant science, agriculture, food, wine and natural resources.

We are focused on delivering high quality customer support, from initial consultation through to analysis of results. Our in-house research scientists will provide advice on experimental design and optimal use of technology, backed by a cross-disciplinary team including experts in agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics.

Our Adelaide facility contains four large areas, referred to as Smarthouses, fitted with conveyor systems and imaging stations (LemnaTec Scanalyzer 3D) for the automated, high-throughput, non-destructive phenotyping of plants. This system consists of over 1km of conveyors with a total capacity of up to 2,400 plants in radio-tagged carts. These are delivered automatically to digital imaging and watering stations controlled by high capacity computing equipment:

  • Visible light images (RGB) allow the measurement of shoot area and inferred mass, plant height and width, canopy density, other morphometric data, leaf colour and senescence.
  • Steady-state fluorescence imaging with blue light large field excitation (<500 nm) allows quantification of plant senescence, chlorosis and necrosis.
  • Programmable watering to weight of plants to enable large scale experiments requiring controlled watering levels.

Research projects facilitated by this technology vary from large scale screening of early growth, salinity tolerance to water and nutrient use efficiency. Possible applications are diverse with respect to the measured traits and plant species studied.

Our purpose-built facility also houses state-of-the-art greenhouses, growth rooms and laboratories.

Field phenotyping services are offered in partnership with the Unmanned Research Aircraft Facility (URAF) at the University of Adelaide. Plans to offer aerial phenotyping via Airborne Research Australia (ARA) and ground-based phenotyping are being developed with input from potential users to align with grant applications.

Our Adelaide facility provides a suite of analytical tools to support phenotyping in either controlled environments or in the field including data capture through Zegami which allows users to filter, sort and chart data from experiments undertaken in our Smarthouses, with the unique feature of being able to group that data with the corresponding images. Our statisticians and data analytics specialists in Adelaide can provide advice on experimental design and support on data analysis.

Our Adelaide team

Dr Bettina Berger
Dr Bettina BergerScientific Director
P +61 8 8313 0825

Plant science is a lifelong passion for our green goddess, Bettina. She is your first port of call for initial consultation and advice on experimental design.

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Helli Meinecke
Helli MeineckeAPPF Executive Officer & Adelaide Managing Director
P +61 8 8313 0808

Fit, fast and fun, our uber queen, Helli, steers our ship with all things related to business management and keeping us on track.

Dr Trevor Garnett
Dr Trevor GarnettDirector Technology Development
P +61 8 8313 1134

Elbow deep in dirt, Trevor loves nothing more than to get his hands on a bit of nitrogen. He provides experimental consultation and guidance on phenotyping technology use and development.

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Jo Pitman
Jo PitmanSenior Marketing Officer
P +61 8 8313 0159

Whether it’s global exploration or a tour of the Smarthouses, Jo loves new discoveries and sharing the stories. She makes sure we look good wherever we appear and promotes our good work and the research at the APPF to the world.

Evi Guidolin
Evi GuidolinAdministrative Officer
P +61 8 8313 1137

Firmly at the helm of all things ‘organisation’, our team would be lost without Evi. She manages our client bookings and all things administration.

George Sainsbury
George SainsburySoftware Engineer
P +61 8 8313 0824

Multi-screen, multi-gaming, multi-tech, up-all-nighter, George takes care of our data management, from storage to tools for database queries and sharing, and everything in between.

Dr Chris Brien
Dr Chris BrienSenior Biostatistician
P +61 8 8313 0824

So smart with all things numbers it makes our heads hurt, Chris helps us mere mortals understand what great experimental design and analysis is, and how to get the best out of it.

Dr Nathaniel Jewell
Dr Nathaniel JewellBiostatistician
P +61 8 8313 0826

With a head for numbers and an encyclopedic memory for facts, Nathaniel will help you obtain the data and graphs you need to interpret your research results.

Dr Guntur Tanjung
Dr Guntur TanjungMechatronic Engineer
P +61 8 8313 1099

You’ll need some serious imaging equipment to capture this tennis ace. Guntur keeps a watchful eye on our phenotyping systems and analyses the images collected.

Paul Jenkins
Paul JenkinsMaintenance Manager
P +61 8 8313 0822
M +61 (0)449 904 536

The oil that keeps the cogs turning, Paul keeps us running like an F1 race car. From lighting to mechanical equipment and the very building we work in, Paul makes sure our plants (and the team) have the perfect environment they need.

Robin Hosking
Robin HoskingHorticulture Manager
P +61 8 8313 0809
M +61 (0)429 900 880

Forget about green thumbs, Robin is widely rumoured to be green from the waist down! He oversees management of the greenhouses, critters (good and bad) and the health and safety of all who step into our domain.

Lidia Mischis
Lidia MischisSenior Technical Officer
P +61 8 8313 0827
M +61 (0)432 297 838

Sweet as a rose, there is nothing plant whisperer Lidia can’t grow. She keeps a watchful eye over the plants in our greenhouses and provides support and wisdom to the humans growing them.

Nicky Bond
Nicky BondTechnical Officer
P +68 8 8313 0771
M +61 (0)421 803 735

As sharp on the court (as Guntur well knows) as she is with a needle, Nicky will be there to provide support in the greenhouses throughout your experiment.

Fiona Groskreutz
Fiona GroskreutzTechnical Assistant
P +61 8 8313 1097

Our princess of bling, Fiona brings her own form of sunshine to the greenhouses as she checks on plants and provides a helping hand to the experiments.

Nick Hanson
Nick HansonPhD Student
P +61 8 8313 1102

Taller than Jack’s beanstalk, Nick is our high achiever in more ways than one, seeking to discover new wheat cultivars that demonstrate the most efficient use of nitrogen.

Brooke Schofield
Brooke SchofieldPhD Student
P +61 8 8313 0824

With hyperspec vision, team sweetheart Brooke, peers into the souls of plants, aiming to develop non-destructive, accurate imaging techniques that are cost effective and easily repeatable.

Canberra (CSIRO)

The High Resolution Plant Phenomics Centre (HRPPC) at CSIRO

The HRPPC combines expertise in plant science and engineering to develop and build (i) cutting-edge phenotyping technologies to support medium throughput phenotyping of model and potted plants in controlled environments, and (ii) novel plant phenotyping solutions to support research experiments at large scale and high throughput in the field. Field applications include ground and aerial platforms with a capacity of over 250,000 plots p.a. and the first high-resolution plant phenotyping capability for glasshouse/field environments – the Cropatron.

The strong mechatronics and software engineering capability at the HRPPC is driving R&D into the  development of cutting edge phenomics technologies that benefit a range of new industries, e.g. pharmaceutics. The centre focuses on troubleshooting and refining existing platforms, e.g. by integrating advanced sensor technologies, to measure new traits in new crops and to keep pace with the demand for deeper insight into plant behaviour and function. Centre engineers have developed phenoSMART™, a science gateway  that provides a national data service for on-demand phenotyping analysis.

We have personnel covering a broad range of expertise from agricultural engineering, to software engineers, mechatronics engineering to logistics and experimental design.

A range of services are available in the controlled environment space, from plant establishment in growth cabinets right through to high resolution imaging of material in our PlantScan, CabScan and TrayScan systems.

We offer a range of high throughput field phenotyping services including, airborne thermal and RGB imaging from our HeliPod system, ground based Phenomobile Lite LiDAR assessment as well as ArduCrop canopy temperature measurements

Our software engineering team at offer tailored data analytics solutions for phenotyping experiments. These are delivered through the cloud based PhenoSMART platform as well as data and metadata management through PODD.

Our Canberra (CSIRO) team

Dr Xavier Sirault
Dr Xavier SiraultDirector
P +61 2 6246 4952

Decadent, unique, luxurious… and that’s just his truffles! Xavier leads our team with a particular passion for automated phenotyping, analytics and especially innovation.

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Dr Michael Schaefer
Dr Michael SchaeferHead Phenomics & Logistics
P +61 2 6246 5632

Adoring Dad, Mick’s passion for pasture feed is no fodder for water cooler chat. His key focus is on phenomics research for applications in breeding and agricultural systems.

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Peter Kuffner
Peter KuffnerLead, Hardware
P +61 2 6246 4933

Avid historian, Peter leads our hardware engineering team in our efforts to create innovative phenotyping instruments in the prototype workshop and keeps a close eye on the smooth running and maintenance of our equipment.

Wayne Thompson
Wayne ThompsonLead, Controlled Environments
P +61 2 6218 3699

Quick with a big smile, global traveller and keen cyclist, Wayne oversees logistics and supports users of our controlled environment services.

Jamie Scarrow
Jamie ScarrowLead, Field
P +61 2 6246 4647

Handy with his hands, if it needs building or fixing, Jamie is your man. When not tooled up, Jamie is busy overseeing logistics and technical services for our field phenotyping projects.

Dr Warren Creemers
Dr Warren CreemersLead, Software
P +61 2 6218 3508

When not exploring his passion for woodwork, robotics and everything in between, Warren leads our software and image analysis team.

Robert Fulton
Robert FultonSoftware Engineer
P +61 2 6218 3505

Robert is happiest camping and rambling about the countryside. If he’s not roaming the great outdoors, he’ll be camped out in the office taking care of our system interfaces and automating data pipelines.

Michanne Aunela
Michanne AunelaTechnical Assistant
P +61 2 6246 5067

With a passion for visual art and gardening, and a sharp eye for detail, Michanne provides technical support to clients and staff in the controlled and field environments.

Michael Salim
Michael SalimMechatronics Engineer
P +61 2 6246 5188

Our resident ‘zen-gineer’, Michael ensures the smooth running of our field equipment and loves designing and constructing innovative hardware prototypes of the future.

Dr Geoff Bull
Dr Geoff BullSoftware Engineer
P +61 2 6218 3502

When Geoff can tear himself away from the crisp white ski slopes of a mountain he works on software development for computer vision related tasks.

Dr Xun Li
Dr Xun LiSoftware Engineer
P +61 2 6246 5067

Keen reader, video gamer and avid traveller, Xun works alongside Geoff, also developing software for computer vision related tasks.

Raj Balla
Raj BallaSystems Administration
P +61 2 6218 3518

Suspected of having a computer screen surgically attached to his person, our office nethead, Raj, takes care of IT infrastructure management and operations support.

Vidya Bala
Vidya BalaSoftware Engineer
P +61 2 6246 4195

At work Vidya focuses on our data management and software development, but in her spare time she enjoys TV shows, bushwalks and gaming.

Sakda EamkulworapongSoftware Engineer
+61 2 6218 3523

Cars have more than just good looks in Sakda’s opinion; he loves their ‘brains’. Sakda has a fascination for ECU remapping, PCB design and micro-controller programming, smarts that come in handy when implementing and troubleshooting software for us.

Louise O'Brien
Louise O'BrienTechnical Services Coordinator
P +61 2 6246 5013

Passionate about the arts and learning from her background in museum education, Louise provides support and logistics in business operations, administration and technical services.

Jordie Ellis
Jordie EllisResearch Technician Trainee
P +61 2 6218 3574

Giving our fellow screen lovers a run for their money, by night Jordie is an avid gamer and TV show junkie. During the day though, he is hands on, assisting with lab and field work.

Canberra (ANU)

Phenomics Facility at ANU

The APPF node at the Australian National University (ANU) has unique expertise in phenomics, bioinformatics, hardware and software development and data visualisation. This provides essential research support to APPF customers, linking phenomics data to underlying genomic variation. The node offers modern PC2 facilities and provides the only quarantine certified plant growth facilities in the ACT region. With a strong history of supporting ground-breaking plant research, including the development of open source, high throughput phenomics infrastructure and visualisation tools, the node creates open data sets for plant science researchers nationally and internationally.

Strategically placed in the Plant Science Division at the ANU, the node benefits directly from the diverse expertise locally available as well as supporting research and technology development at the Research School of Biology. This includes two Centres of Excellence (CoE): the ARC CoE in Plant Energy Biology (PEB) and the ARC CoE for Translational Photosynthesis (TP). Additional collaborations are in place with the ANU-CSIRO Centre for Biodiversity Analysis, the CoE for Robotic Vision and the National Computational Infrastructure (NCI), which offers high-performance supercomputing, cloud and data repository.

Multidisciplinary in-house experts at our ANU node can assist with experimental planning and design, bioinformatics, image and data analysis, and genomics related to phenomics (including GWAS and GBS). We specialise in developing open source, low cost phenotyping solutions, data management, machine learning applications for phenotyping, next generation data visualisation and virtual reality. Collaborative opportunities are also possible with our location partners ARC Centres of Excellence, Plant Energy Biology and Translational Photosynthesis.

Our ANU node consists of a modern greenhouse facility, growth cabinets and, coming in 2018, a modular growth environment facility. The greenhouse facility includes precision environmental control and top down RGB real time imaging of plant growth to analyse genetic variation in water use efficiency in plant growth. It also incorporates a glasshouse Balance Array (real time pot weighing system). Conviron plant growth cabinets include the Spectral Pheno Climatron (SPC) chambers equipped with 7 Heliospectra LEDs and 10 bands LED lights, top down NIR, DSLR RGB, time lapse imaging and simulated climate control. The modular growth environment facility consists of 4 cutting edge modular growth environments for precision phenotyping with dynamic light, temperature, moisture and nutrients levels, simulating current and future conditions.

In the field, our ANU node can conduct remote sensing experiments that measure growth and phenology (seasonal development) of most leaves in a canopy with virtual/augmented reality to visualise across scale, space, time and colors, leading to predictive models for selecting and breeding.

Our ANU facility offers a number of phenomics analytics services including:

  1. An end to end interface for experiment and chamber scheduling, project management, monitoring and data visualisation.
  2. Segmentation pipeline with:
    • automated QA/QC steps for ensuring clean datasets and error notification
    • image calibration and color correction and automated segmentation
    • automated output of phenotypes at the plant level, eg rosette area, compactness, roundness, eccentricity, RGB metrics for small flat plants like Arabidopsis, Tobacco, etc.
  3. TraitCapture genomics analysis pipeline (all data can be readily accessed via the TraitCapture portal):
    • trait heritability over time and environment
    • multi-trait co-heritability over time and environment
    • quantitative trait locus mapping (GWAS)

Our Canberra (ANU) team

Dr Tim Brown
Dr Tim BrownDirector
P +61 2 6125 2644

Someone who can certainly ‘see the forest for the trees’ is Tim. His love of forests and the cutting edge technology that allows us to ‘virtually’ see them from the sky down to the molecule, knows no bounds. When not attached to a VR headset, Tim focuses on our technological development and research collaborations.

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Alyssa Weirman
Alyssa WeirmanBusiness Manager
P +61 2 6125 8319

Rock loving, fossil fossicking Aly is at the very bed rock of our team. She focuses on business development, facility administration and generally making things happen.

Prue Kell
Prue KellTechnical Officer
P +61 2 6125 6961

Prue can’t get enough of plants! Each day she manages our growth cabinet facility, supporting users with advice, planning and compliance, before heading home to give her garden the same passionate care.

Gareth Dunstone
Gareth DunstoneComputational Systems Developer
P +61 2 6125 2644

Rumoured to live with a large grey and white lion, when not gaming the night away, Gareth oversees our systems development, coding and programming.

Argyll McGhie
Argyll McGhieWeb developer
P +61 2 6125 2644

When he isn’t globetrotting and dining out (where’s our invitation?!), Argyll is busy keeping a tight eye on the ongoing development and maintenance of the Traitcapture portal and plant phenomics software.

Richard PoireSenior Technical Officer
P +61 2 6125 4492

Our part-time model (try to spot Richard in photos on our website), long distance runner and makerspace aficionado, Richard is a plant physiologist and phenomics expert for our team.

Ellen Levingston
Ellen LevingstonTechnical Officer
P +61 2 6125 2644

When not rocking out with her synths or curating her culinary garden collection, Ellen is knee deep in data, from maintaining sensors to database design and exploration of new cutting-edge data technology.

Penny BurrellTechnical Assistant
P +61 2 6125 8319

Not sure where to start?  Let’s talk…

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