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.
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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. Watch more here.
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 greenhouses, 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:
- Hyperspectral imaging (350-2500 nm) utilising Specim cameras integrated onto the high throughput platform by WIWAM.
- 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.
In addition our purpose-built facility also houses:
- A specialised heat and drought phenotyping capability – the first of its kind in Australia – will be available. This unique capability will consist of two new controlled environment rooms (CERs) fitted with programmable LED lighting and DroughtSpotters. The specially fitted CERs, each with a capacity of 98 plants, will enable experiments to investigate two different climate regimes in parallel, with up to seven variables including light quality, CO2, humidity, heat and drought stress. Construction is underway, with the new specialty rooms expected to be available to researchers in the second half of 2018.
- The DroughtSpotter – A specialised greenhouse fitted with LED lighting and a high precision, fully automated gravimetric platform with programmable irrigation to assess transpiration dynamics of plants with a precision of up to 1g. The integrated irrigation units allow precise and reproducible water application for drought stress or related experiments that require an accurate control of water volume to 1ml.
- 33 state-of-the-art greenhouses
- 13 growth rooms, and
UAV based field phenotyping services are offered in partnership with the Unmanned Research Aircraft Facility (URAF) at the University of Adelaide. Hyperspectral imaging from the air is offered in collaboration with Airborne Research Australia (ARA). Hyperspectral imaging from a ground-based phenotyping platform will be available early in 2019.
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
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 of cutting edge phenomics technologies that benefit a range of new industries, e.g. pharmaceutics. The centre focuses on supporting and refining existing platforms, for example 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, an innovation to increase capabilities. Our 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
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:
- An end to end interface for experiment and chamber scheduling, project management, monitoring and data visualisation.
- 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.
- 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)