Plant phenotyping technology
The technologies and expertise developed by the APPF are world-leading, internationally recognised and have ensured Australian science is an attractive partner for international collaboration.
Phenotyping in Greenhouses
The APPF provides the full spectrum of modern growth facilities, from temperature controlled greenhouses through to state-of-the-art, automated, high-throughput and deep phenotyping technology in large-scale Smarthouses. See two sections below for further information on our greenhouse and growth room facilities and some additional, unique phenotyping technology available in some of these controlled environments.
Greenhouses
High-throughput Smarthouses
- Location: Adelaide.
- Suitable for: All plant types ranging in size from 10cm through to 1m in height.
- Key features:
- Lemnatec based, automated phenotyping greenhouses
- Non-destructive measurement of growth using RGB, fluorescence and hyperspectral imaging
- Automated watering to weight
- Pot capacity up to 4.5kg
- Four rooms, each with 600 plant capacity (@ 2.5kg pot weight), total plant capacity 2,400
- Quarantine approved capacity for 1,200 plants
- Hyperspectral imaging: Download the factsheet.
- Smarthouse specifications: Download the factsheet.
- For more information: Please contact our experts to discuss how your research might benefit.
- Pricing & availability: Please contact us by e-mail or on +61 8 8313 1137.
- To book: Please submit a booking form.
The largest high-throughput phenotyping facilities in the southern hemisphereThe Plant Accelerator contains four large greenhouses, referred to as Smarthouses, fitted with conveyor systems and imaging stations (LemnaTec Scanalyzer 3D) for the 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.
- Specim VNIR and SWIR hyperspectral cameras to capture the spectral reflectance of plants from 350-2500 nm. The hyperspectral reflectance data can be used to non-destructively measure a whole range of plant constituents, including nutrients, water or other aspects of plant physiology as long as a distinct spectral signature can be analysed.
- 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.
The APPF offers a range of greenhouses for hire in Adelaide and Canberra
Greenhouses – Adelaide
- Location: Adelaide.
- Suitable for: All plant types.
- Key features:
- Excellent temperature control in standard greenhouses
- Specialty greenhouses with specialised temperature and humidity control (i.e. rice growing rooms)
- Wireless monitoring of temperature, humidity (standard) and light (optional)
- Supplemental LED lighting available in some greenhouses
- Quarantine approved greenhouses available
- For more information: Please contact us by e-mail or on +61 8 8313 1137.
- To book: To make a booking, please submit a booking form.
- Procedure for growing non-GM plants information sheet.
The Plant Accelerator contains 34 greenhouses in PC2 and non-PC2 areas ranging in size from 24 to 48 and 72 sqm. Some greenhouses are quarantine approved to allow plant growth from imported seeds.The greenhouses are fitted with evaporative and/or refrigerated cooling. Variance in temperature in the greenhouse can be pre-programmed to reflect external conditions (e.g. cool nights, moderate mornings, hot afternoons).The greenhouses’ double glazed acrylic skin provides good insulation properties and transmits the entire spectrum of UV light, ensuring that internal environmental conditions are as close as possible to those in the field.
Greenhouses – Canberra (ANU)
- Location: Canberra (ANU).
- Suitable for: all plant types.
- For more information: please email or phone +61 2 6125 3652.
The APPF at ANU hosts a modern greenhouse facility consisting of 6 rooms which 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. A glasshouse balance array has also been developed which provides real time pot weighing services to clients. You can view some demonstration data of the weighing system on this here.
Phenotyping in greenhouses
DroughtSpotter
- Location: Adelaide.
- Suitable for: All plant types.
- Key features:
- Phenospex gravimetric watering system in greenhouse
- Pot capacity up to 12kg
- Individual watering and monitoring of 168 plants
- Supplemental LED lighting
- For more information: Please contact us by e-mail or on +61 8 8313 1137.
- To book: Please submit a booking form.
- Non-GM procedure for growing non-GM plants in the DroughtSpotter information sheet.
The DroughtSpotter is a gravimetric platform with precision 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. The individual pot weight can be up to 12kg.The platform is installed in an existing greenhouse and comprised of 168 load cells for which watering protocols or drought scenarios can be easily customised. The designed irrigation events maintain the target weight of each individual plant pot according to the researchers’ experimental protocol and provide plant transpiration rates at high temporal resolution calculated by the loss of weight.
PlantEye 3D laser scanner
- Location: Adelaide.
- Suitable for: All plant types.
- For more information: Please contact Trevor Garnett to discuss how your research might benefit.
- Pricing & availability: Please contact us by e-mail or on +61 8 8313 1137.
- To book: Please submit a booking request.
PlantEye uses a laser light section to acquire 3D point clouds of plants. It projects onto the plant or plant canopy a very thin near-infrared laser line, which is reflected and captured with an integrated camera that is mounted at the other end of the PlantEye sensor. The projected laser line shifts based on its distance towards the sensor, and a record of those shifts is then used to generate a height profile of the plant. By moving the sensor over the plant, or by moving the plant relative to the sensor, you get multiple height profiles which are merged together to form a 3D model of the plant. In a second step, the sensor segments this 3D model, recognizes plant organs and computes a diverse set of morphological plant parameters within less than a second.
Time Lapse
- Location: Canberra (ANU).
- Suitable for: all plant types.
- Key features:
- For more information: please email or phone +61 2 6125 3652.
More information to come.
Growth chambers and rooms
Both APPF locations offer state-of-the-art growth chambers and rooms, with a range of phenotyping capabilies including TrayScan, PlantEye and hyperspectral scanning.
Growth chambers and rooms
Drought + heat phenotyping platform
- Location: Adelaide.
- Suitable for: All plant types.
- Key features:
- Twin Conviron CERs with control of vapour pressure deficit (VPD), light quality and intensity, enable parallel experiments with different climate regimes giving unprecendented ability to apply drought and heat stress to plants while measuring transpirational response
- Each chamber is specially fitted with temperature and humidity control (5-50°C, 40-80%), variable wavelength LED lighting up to 1000 µE.m-2.s-1 and Phenospex gravimetric watering systems
- Individual watering and monitoring of 96 plants in each room with individual pot capacity up to 15kg
- Specifications: Download the factsheet.
- For more information: Please contact us by e-mail or on +61 8 8313 1137.
- To book: Please submit a booking form.
This unique capability consists of two Conviron controlled environment rooms (CERs) specially fitted with temperature and humidity control, variable wavelength LED lighting up to 1000 µE.m-2.s-1 and Phenospex DroughtSpotters. DroughtSpotters are fully automated gravimetric platforms with high precision irrigation to 1ml, enabling the maintenance of target weights of individual plant pots according to the researchers’ experimental protocol and the calculation of plant transpiration rates at high temporal resolution based on weight lost. The unique twin CERs, comprising 96 load cells per room, enable parallel experiments for which watering protocols or drought scenarios can be easily customised. The individual pot weight can be up to 15 kg.
Growth chambers and rooms
Controlled environment growth chambers and rooms are designed to provide precision climates (e.g. programmable temperature, lighting and humidity). These are available for use at all of our locations.
Growth chambers and rooms – Adelaide
- Suitable for: Model through to crop plants.
- Key features:
- Walk-in and reach-in Conviron growth chambers
- Light intensity variable up to 1000 µmol.m-2.s-1
- CO2 control in small and large growth rooms
- Specifications: Information about lighting, temperature and layout specification sheet.
- For more information, pricing and availability: Please contact us by e-mail or on +61 8 8313 1137.
- To book: Please submit a booking form.
The Plant Accelerator offers a number of environmentally controlled growth rooms and growth chambers in PC2 and non-PC2 areas. The growth areas of the walk-in-rooms range from 7, 11 to 20 sqm, whilst the reach-in chambers have a growth area of 2 sqm. Additive humitidy is available in all rooms, whilst some of the rooms have additive CO2.
Growth chambers and rooms – Canberra (ANU)
- Suitable for: small plants and seedlings.
- For more information: please email or phone +61 2 6125 3652.
The APPF at ANU has a range of Conviron plant growth cabinets enabling research projects that require accurate climate controlled environments. Standard 1-tier and 3-tier growth cabinets are available as well as enhanced Spectral Pheno Climatron (SPC) chambers. These enhanced chambers are equipped with 7 Heliospectra LEDs and 10 bands LED lights, top down nIR, DSLR RGB and time lapse imaging and simulated climate control.
SpectralPhenoClimatron (SPC) and Traitcapture
- Location: Canberra (ANU)
- Suitable for: A wide range of plants from seedlings to mature wheat, rice, tobacco, tomates, etc.
- Key features:
- Real-time climate control of chambers that can replicate any natural environment dynamically (5 – 40 degrees celsius)
- 5 minute interval 24/7 time-lapse imaging
- TraitCapture “seeds to traits” phenotyping pipeline (for flatter plants like arabidopsis and tobacco)
- For pricing, availability or more details: please email or phone +61 2 6125 3652.
The SPC climate chambers provide real-time climate control, replicating any natural environment dynamically (for example the chamber can replicate the conditions of an environment from sunrise to sunset including light spectrum changes). The high throughput system enables visual growth phenotyping of up to 320 plants per chamber in 7 climate chambers. SolarCalc software controls light intensity and color, temperature and humidity at 1-minute intervals. This enables the creation of dynamic growth conditions with diurnal and seasonal cycles from any location.
TraitCapture
TraitCapture is a “seeds to traits” pipeline which allows users to track seed/genotype selection, set growth conditions, and analyze phenotypic variation for heritable components through to mapping causative loci via GWAS and QTL analysis.
Possible experiments include:
- Iterative QTL identification and tests of pleiotropy
- Heritability of potential spectral indices using hyperspectral cameras
- Spatial and temporal distribution of fluorescent pigments under environmental stress
- Light and temperature interactions on transpiration using Infrared (IR) cameras
- Genetic basis of photosynthetic activity and efficiency using chlorophyll fluorescence cameras
- Integration of 2.5D and 3D quantification of plant growth with stereo imaging
Growth Capsules – Canberra (ANU)
Our first Growth Capsule has arrived and is undergoing set up and testing. The balance will arrive early 2019. These capsules are another excellent capability for phenotyping plants in a fully controlled environment. We will update this page once our Growth Capsules are ready for hire.
- For more information: please email or phone +61 2 6125 3652.
Phenotyping for growth chambers and rooms
Hyperspectral scans
Hyperspectral scanning is available in conjunction with the growth chambers and rooms, as well as the SpectralPhenoClimatron chambers.
In the field
Mobile field phenotyping
Field phenotyping with UAVs/drones and manned aircraft
UAV/drone/manned aircraft field phenotyping is available across the three APPF nodes.
Adelaide
- Location: Adelaide
- Suitable for: All crop plants.
- Key features:
- Multiple platforms available: UAV/drones and manned aircraft
- Experienced, licensed UAV pilots
- Hyperspectral, RGB, multispectral and thermal imaging
- Data pipelines
- Hyperspectral imaging and data analysis: Download our factsheet.
- For more information: Please contact us by e-mail or on +61 8 8313 8136.
- Research project requests: Please complete and submit the booking form.
- For training.
In partnership with the URAF (the University of Adelaide Unmanned Research Aircraft Facility), we provide improved phenotyping capabilities to support plant and agricultural science. Platforms range from multi-copters to fixed wing aircraft, carrying cameras and multispectral and thermal sensors. Images captured produce GIS layers used to integrate with field data to further develop relationships between plant growth, environmental conditions and plant treatment. The potential to measure parameters on field trials such as establishment, height, biomass, stress and nutritional status can be explored using this technology. As part of the ARC Wheat Hub, methods are being developed to enable phenotyping of single row plots.
Canberra (ANU)
FieldExplorer
- Location: Adelaide.
- Suitable for: A variety of crops less than 1.3m in height. Rugged field conditions.
- Key features:
- Non-destructive phenotyping
- Tough, durable agricultural grade platform suitable for a variety of field conditions
- Sensors onboard include RGB, LiDAR, GPS/INS and two hyperspectral cameras
- Easy to use and intuitive interface provides real time position/orientation of the platform and in relation to plots.
- Lightweight and mobile for use in the field
- Specifications: Download our factsheet.
- For pricing, availability or more details: Please contact us by email or on +61 8 8313 8136.
The FieldExplorer brings capability to accurately measure the performance of plants in different environments non-destructively and over time, giving a greater ability to measure critical information about crop growth and health in field trials such as biomass, nutrient content and stress responses.
The high resolution imaging module enables consistent and precise data collection across trial sites. Supplementary halogen lighting provides consistent imaging conditions all day regardless of cloud cover.
The FieldExplorer combines LiDAR, enabling 3D reconstruction of a plant canopy and biomass estimates, with visible-near infrared (VNIR) and short-wave infrared (SWIR) hyperspectral imaging (400-1700 mm) and high resolution RGB imaging.
Easy loading of plot files and simplified automated data storage of all sensor data in annotated plot files, plus calibration and system information logging allows simplified data analysis.
Specialised software enables single pixel level mining and sensor data fusion, based on pre-defined plot coordinates derived from GPS/INS for precision and accuracy.
The open data format enables connection to third party analysis platforms to maximise data utility and flexibility.
Portable phenotyping devices
Photosynthesis
LICOR 6400 photosynthesis system
- Location: Canberra (ANU).
- Suitable for: Most crops and plant applications. Field and laboratory measurements.
- Key features:
- Complete solution – measures fluorescence and gas exchange simultaneously over the same leaf area with full control of environmental variables
- Precise and accurate – measure small photosynthesis rates and CO2
- Portable – laboratory-quality measurements in a field-portable system
- For more information on the LICOR 6400 photosynthesis system.
- For pricing, availability or more details: please email or phone +61 2 6125 3652, or go to our booking website.
These instruments are rugged, portable, offer a high level of software and hardware integration as well as being renowned as the world leader in portable photosynthesis measurement systems.
Chlorophyll
Fluorometers
Walz MONITORING-PAM chlorophyll fluorometer
(Long term measurement)
- Location: Canberra (ANU).
- Suitable for: Most plants and leaf types.
- Key features:
- Suitable for long-term measurements
- Modulated chlorophyll fluorescence
- For more information on the Walz MONITORING-PAM chlorophyll fluorometer.
- For pricing, availability or more details (ANU): please email or phone +61 2 6125 3652, or go to our booking website.
The chlorophyll fluorometer MONITORING-PAM is designed for unattended, long-term and multi-site monitoring of chlorophyll fluorescence in air or underwater. At each measuring site, compact and robust emitter-detector units measure modulated chlorophyll fluorescence and perform saturation pulse analysis.
Meters
FieldScout CM 1000 chlorophyll meter
FieldScout CM 1000 chlorophyll meter- Location: Canberra (ANU).
- Suitable for: Most plants and leaf types.
- Key features:
- Instant measurement of relative chlorphyll content
- Detects stress earlier than visual monitoring
- Laser guides to display outline of measured area
- Handheld
- Non-contact
- For more information on the FieldScout CM 1000 chlorophyll meter.
- For pricing, availability or more details: please email or phone +61 2 6125 3652, or go to our booking website.
This handheld device is lightweight, quick and easy to use for chlorophyll content measurements.
Photon Systems Instruments PlantPen PRI 200 & NDVI 300
- Location: Canberra (ANU).
- Suitable for: Most plants and leaf types.
- Key features:
- Very lightweight
- Relative chlorophyll content measurement
- For more information on the PSI PlantPens.
- For pricing, availability or more details: please email or phone +61 2 6125 3652, or go to our booking website.
PlantPen is a reflectance-based device that provides a convenient, low-cost method of measuring the relative chlorophyll content of a leaf sample. PlantPens measure and calculate particular reflectance indices to assess chlorophyll content, protoprotecting carotenoids, and other important features in live foliage. Two standard Plant Pen versions measure the most common indexes: PRI and NDVI.The PlantPen model PRI 200 measures Photochemical Reflectance Index in two narrow wavelength bands centered close to 531 nm and 570 nm. PRI is sensitive to changes in carotenoid pigments that are indicative of photosynthetic light use efficiency, the rate of carbon dioxide uptake, or as a reliable water-stress index. As such, it is used in studies of vegetation productivity and stress.The PlantPen model NDVI 300 measures Normalised Difference Vegetation Index, which is an important indicator of chlorophyll content in plants. The device compares reflected light at two distinct wavelengths, 660 and 740 nm. The pigment in plant leaves – chlorophyll – strongly absorbs visible light (from 0.4 to 0.7 μm) for use in photosynthesis. The cell structure of leaves, on the other hand, strongly reflects near-infrared light (from 0.7 to 1.1 μm). The differences in plant reflectance in the visible and near-infrared wavelengths are used to calculate NDVI index. NDVI is directly related to the photosynthetic capacity and hence energy absorption of plant canopies.
Light
LICOR Li-191 quantum line sensor
- Location: Canberra (ANU).
- Suitable for: Most crops and plant applications. Field and laboratory measurements.
- Key features:
- Quick measurement of under canopy light
- Consistent measurements
- For more information on the LICOR Li-191 quantum line sensor.
- For pricing, availability or more details: please email or phone +61 2 6125 3652, or go to our booking website.
The LI-191R Line Quantum Sensor measures PAR integrated over its 1-meter length. It is used to measure sunlight under a plant canopy, where the light field is non-uniform. The LI-191R makes it easy to measure under-canopy light in many plots quickly and consistently. It measures light in units of Photosynthetic Photon Flux Density (PPFD), which is expressed as μmol s-1 m-2.
Leaf transpiration
Decagon Devices SC-1 leaf porometer
Decagon Devices SC-1 leaf porometer- Location: Canberra (ANU).
- Suitable for: Most plants and leaf types.
- Key features:
- Measurement of stomatal conductance
- Accurate and lightweight
- Portable
- For more information on the Decagon Devices SC-1 leaf porometer.
- For pricing, availability or more details: please email or phone +61 2 6125 3652, or go to our booking website.
The SC-1 Leaf Porometer determines the stomatal conductance by measuring the vapour flux from the leaf through the stomates. Readings can be displayed as either conductance or resistance and saved for downloading later.
Delta-T AP4 leaf porometer
Delta-T AP4 leaf porometer- Location: Canberra (ANU).
- Suitable for: Most plants and leaf types.
- Key features:
- Direct readout of stomatal conductance or stomatal resistance
- For more information on the Delta-T AP4 leaf porometer.
- For pricing, availability or more details: please email or phone +61 2 6125 3652, or go to our booking website.
The AP4 Leaf Porometer measures diffusion conductance by comparing the precise rate of humidification within a small cuvette (chamber) to readings obtained with a calibration plate. The plate has 6 diffusion conductance settings whose values have been accurately determined by finite element analysis.
Leaf area
LICOR leaf area meter 3000C
LICOR leaf area meter 3000C- Location: Canberra (CSIRO).
- Suitable for: Most crops and plant applicationsin the field and laboratory.
- Key features:
- Simple fast and accurate
- Non-destructive leaf area measurement
- lightweight
- For more information on the LICOR leaf area meter 3000C.
- For pricing, availability or more details: Please contact us by email or on +61 2 6218 3430.
- Request for service: To submit a project please complete the request for service form.
The LI-3000C combines an easy-to-use readout console with the proven scanning technology of the LI-3000C sensor head to provide a powerful system for portable, non-destructive leaf area measurements. It utilizes an electronic method of rectangular approximation to provide 1 mm2 resolution. Leaf area, leaf length, average width, and maximum width are logged by the readout console as the scanning head is drawn over a leaf. Files can be viewed on the display or output to a computer using the LI‑3000C application software.