Digital phenotyping explained
WPS has broken down the process to provide a better understanding of the digital plant phenotyping system. The numbers in the picture are explained below.
1. Experimentation Control Software
The WPS Experimentation Control Software gives the user the ability to seamlessly integrate and initiate phenotyping experiments. The software provides flawless control over measurement settings, task scheduling, irrigation and plant information management. Is also provides the basis for data handling, analysis and reporting.
2. Large growth area
The large growth area is the buffer where plants are stored in between imaging. Therefore, the area functions both as growing area and storage. These growth areas are highly adaptable, giving flexibility in plants and used space.
3. Small growth area
A small growth area along with a large growth area provides the user with extra flexibility. The small buffer can be used for smaller or shorter experiments, as well as different crops, alongside the larger experiments.
4. Manual loading area
To give researchers the freedom to spontaneously image a handful of plants, the manual loading area can be added. The individual plants plus plants carriers can be manually placed into the system, send to the imaging cabinets and manually removed after imaging.
5. Automatic plant transportation
During the imaging process, plants are automatically transported to the imaging cabinets, whilst being tracked by the RFID tag in the plant carriers. The conveyors are highly adaptable, in size, width and transportation speed.
a) Optional dark adaption tunnel
The dark adaption tunnel can be added to the automatic plant transportation conveyors, for both small and big plants. This is particularly needed when researchers are researching photosynthesis. The plants pause in a fully dark space before moving to the fluorescence camera, this way the best result is measured when fully exposing the plants to light.
6. Watering & weighing unit
Digital Phenotyping is all about controlling one group of parameters to objectively quantify the variation in other parameters. The precision and validation of the irrigation per plant is crucial in this respect. The WPS irrigation module allows the user to very accurately irrigate each individual plant according to the pre-set amounts. This allows the user to very accurately define and apply strict water regimes within the same running experiment and thus have the potential to objectively measure the effects of different watering regimes on the samples.
7. Vision/imaging
a) RGB
RGB imaging remains the workhorse of digital phenotyping sensors producing rapid, easy to interpret data and vital phenomic parameters on morphology, biomass, plant growth, and architecture and (de-) coloration using multiple colored images.
b) IR
Infrared imaging is a common tool for digital plant phenotyping. The sensor creates a pixel-based area of the temperature of the plant, which in turn relates to water usage of the plant. As transpiration decreases due to biotic and abiotic stresses, which is measured by the IR sensor, it is a reliable tool to determine changes to the physiological status of a plant.
c) NIR
NIR imaging is able to penetrate leaf surface. This is advantageous to the researcher because it allows for mapping of the leaf and canopy architecture. This is turn gives the researcher the ability to measure parameters such as leaf thickness and growth habits, as well as yield and growth under stress.
d) Fluorescence
By first pausing the plants during automatic transport in the dark adaption tunnel and subsequently exposing them to full light in the imaging cabinet, the plant’s capacity to assimilate actinic light is measured using the fluoresce sensor. Fluorescence imaging can in turn assess the photosynthesis ability of plants, which is affected by disease and stress to biotic and abiotic factors.
e) Hyperspectral
Hyperspectral imaging is a technique which extracts a very broad range of information from the plant, typically depicted as a ‘data cube’. The data cube consists of multiple images of which each is taken at a narrow wavelength of the electromagnetic spectrum.
f) SS3D
The WPS SmartScan 3D rotates the plant while taking multiple side images that are rendered into a 3D image using a specifically designed algorithm. The software is able to detect numerous parameters, such as flowers and buds for Phalaenopsis.
g) Rotation Unit
The WPS rotation unit still allows ultra-high throughputs and has very high accuracy between the conveyor turntable and the camera angle- allowing up to 70 images in less than 4 seconds with high accuracy and reproducibility. The imaging stations that require plant rotation in order to generate images of different side views are equipped with this high-precision rotation unit.
8. Data storage
Due to the large number of images taken of the plants, data handling and storage is key. WPS systems are fully integrated and can work together with the data storage setup of research facilities, both local or cloud based. Each image is automatically linked the appropriate plant due to the RFID tag in the plant carrier.
9. Data analyses
Once images are acquired and properly stored, the Experimental Control Software allows for detailed image analysis. Reliable imaging and analysis is crucial for the validity of scientific research and is therefore a key focus of WPS.
10. Reporting
A most common bottleneck in phenotyping is reporting. With an almost infinite amount of images, bridging the gap between simply analyzing and actually reporting is key. WPS provides tools that turn almost any data source into interactive, actionable information. Researchers can create powerful, richly formatted, dynamic reports from the database. Reports transform raw data into sophisticated, interactive dashboards that will enable data overviews quicker and more thoroughly.
Download the explanation of the digital phenotyping system as PDF.
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