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The Plant Accelerator
High Resolution Plant Phenomics Centre
Telephone: +61 2 6125 8319
PlantScan provides non-invasive analyses of plant structure (topology, surface orientation, number of leaves), morphology (leaf size, shape, colour, area, volume) and function by utilising cutting edge information technology including high resolution cameras and three-dimensional (3D) reconstruction software.
Currently, there is a disjuncture in scientists’ capacity to measure at the molecular and functional levels. Genomics is providing a huge amount of data retrieved using high-throughput technologies but our ability to measure life at the whole-plant level (Phenomics) has lagged behind. There is, therefore, a need to level the balance between the speed of genotyping and phenotyping. Thus, high-throughput phenotyping tools are becoming vital for research looking at improving crop performance and adapting crop varieties to climate change. By providing an integrated multi-sensing platform with a range of imaging sensors, PlantScan helps restore this balance by increasing researchers’ capacity to precisely and accurately quantify the biological processes involved in the development and functioning of plants and, this, with greater detail, frequency and objectivity than traditional methods.
PlantScan is composed of a double conveyor belt, manually loaded, with plants held in position on pot carriers. Individual plants are identified by bar code. A first transfer station diverts the plant to a split conveyor belt which accurately positions the plant for imaging using laser proximity sensors. A rotating motor, fitted with an incremental encoder with up to 65,536 lines per revolution and mounted on a scissor-lift platform ensures the plant is scanned from every angle. A top-imaging system complements the 3D information collected from the sides. After imaging, the plant is conveyed to a second transfer station before being ejected by an actuator onto a double gravity belt. Plants are then manually unloaded and transported back to their growing environments. All motion control and image acquisition was designed in LabView. The interface was built in a hybrid 32- and 64-bit architecture, which automatically detects the various sensors available to the instrument and provides the user with all configuration options available for specific sensors. PlantScan relies on its modular design for the flexibility to match to the requirements of many different researchers and biological systems. The user may choose the combination of modalities to be measured from:
The software provides a range of feedback on the motion controls, e.g. defective proximity sensors, as well as a graphical interface displaying the location of the pot carriers in the system in real time. During image acquisition, the system is closed to ensure reproducibility of imaging conditions, and avoid any safety hazards from moving parts and the class 2A LiDAR lasers, although the lasers are eye-safe. The light spectrum is generated by fluorescent light run on a 75 kilo-Hertz electrical signal to avoid noise in the acquired images. The light is diffuse to approximate Lambertian conditions within the imaging chamber. The system uses standard industrial components from reliable manufacturers with worldwide service.
PlantScan is able to scan very small seedlings or plants, from a few centimeters to a couple of meters in height and up to a meter thick, with equal accuracy. Data are captured with their contextual information and collated into one multi-layer data file before being stored in a purpose-built database.
An installer containing a set of operators representing the previously mentioned steps has been generated. It contains 3 operators, batch files to run the programs and an initial dataset of meshes. To install the programs, download the exe file bellow , double click on it and follow the installation wizard instructions. Note that the installation path must be somewhere where you have writting permissions (due to output generation). Note that the developpment of the different operators has been done under Ubuntu 10.04 LTS 64-bits.
More information are available in the documentation of the installer. For complementary instructions, please contact Xavier Sirault.
The University of Adelaide
Last Modified 19/01/2017 Helli Meinecke
CRICOS Provider Number 00123M