LemnaTec Scanalyzers provide a comprehensive range of phenotyping research platforms from bench-top enclosures to systems that monitor large fields.
Non destructive Imaging Techniques enable researchers to measure plant growth over time
Growth rate is a very important term to describe plant development over time, in most cases growth development. As long as plants primarily invest their energy in the development of new leaves, the growth curves of leaf areas mainly follow an exponential pattern. Exponential growth is merely an ideal growth pattern, where all energy produced by existing leaves is transferred to new leaves, which again produce energy for additional leaves, and so on. As this is not the case in later stages of plant development, during flowering and fruiting, growth rates will subsequently decrease, so that other growth models may be more appropriate to describe later plant growth stages.
In any case, it is important to acknowledge that almost the worst approach to growth quantification is to simply use the measured values like leaf area, fresh/dry weight or plant height directly. To compare plant growth directly on the basis of this one parameter without taking appropriate transformation steps is problematic, especially if rates (differences between a set of points in time) are to be compared. High and systematic standard deviations or, rather, systematic faults will occur, because a bigger plant at a certain point in time will always have a higher absolute difference in the measured parameter than smaller plants. By using the exponential or other growth models as a first data transformational step, the different start values will be considered appropriately, which in turn results in similar growth rates, even for plants of different sizes.
Shoot Growth Experiment
The data described here originates from an experiment performed on the PhenoFab system containing ten miscanthus genotypes, each in fivefold replicates. The images where acquired and the plants have been watered daily using a High throughput Scanalyzer 3D system and LemnaControl for 35 days. The imaging system was configures to take four lateral views rotated for 90 degrees each and a top view resulting in a total of 8,750 images. Genotypes were equally distributed between and within a total of four conveyor belts in one compartment.
Image Processing with LemnaGrid
The image processing was performed on LemnaGrid. The main aim of this project was the extraction of growth rates. This parameter can be easily extracted using a three step approach. In the first step the background was defined as pure white giving a binary mask, then a region of interest was created to exclude conveyor belts and pots and in a last step the binary mask and the region of interest were combined and the size of the object was calculated. Secondary digital phenotyping traits like circumference, height, convex hull etc. are provided as well using this approach but are not of interest in this application
Data Mining to extract statistical relevant growth rate
The LemnaMiner has been used to take into account different projected areas from the different views for the result. In this case the average projected area of four side views was used to create growth plots and to calculate the growth rate for various plants and the different genotypes. For other species that have a higher projected aerial area such as spinach, tomatos or tobacco this area can be taken into account as well to create a digital biomass. In later on external analysis the tables created by LemnaMiner can be used to model the growth and to identify similarities or differences in growth behavior within or between genotypes (e.g. by k-means-clustering)
- Plant Phenomics
- High Throughput Screening
- Climate Change
- Duckweed Growth Inhibition Test
- Field Phenotyping
- High Content Screening
- QTL Analysis
- Water Use Efficiency
- Abiotic Stress
- Plant Phenotyping, Plant Phenotype
- Controlled Environments
- Energy Crops
- Germplasm Characterisation
- Hyperspectral Imaging
- Root Development
- Smart breeding
- Drought Tolerance
- Environmental Simulation
- Growth Rate
- Non-destructive Plant Phenotyping
- Soil Water Content