RGB Structural Imaging | QubitPhenomics.com

A central feature of any phenomics screening system is the ability to track growth patterns of plants as they progress through developmental stages and/or through the imposition, onset and recovery from stresses. All PlantScreen^TM systems incorporate imaging stations for morphometric analysis of plants, as well as colour analysis.

Morphometric and colour analysis may be conducted with equal effectiveness on monocotyledenous and dicotyledonous plants. Scanning is rapid for high throughput analysis, and automated protocols in software correct for any image distortions and provide accurate data of key morphomteric parameters chosen by the operator. The data are collated with data from other imaging stations, if employed, to correlate changes in growth patterns with physiological responses to imposed environmental conditions.

Key features

2D or 3D scanning mode
Top view up to 150 cm plant height
Side view up to 150 cm plant height
Side view in range 0–360°
Line scanning mode for side view
Species oriented analysis (mono and di-cotyledonous plants)
Static and dynamic analysis
Homogeneous LED light source

RGB images processing

RGB images are scanned with a resolution of 5 to 25MP from three directions (from the sides and from the top). Samples are illuminated with consistent quantity and quality of light. Options are available for the inclusion of novel 3D scanning technology for the most in-depth morphometric reconstruction of plants.

Step 1 (A): Barrel distortion correction

Step 2 (B): Tray detection and cropping

Step 3 (C): Background subtraction

Results (D): Binary and RGB images as input for analysis

Parameters Computed

Leaf Area: Number of pixels covered by the plant surface converted to relevant units. Useful for monitoring growth rate.
Solidity/Compactness: Ratio between the area covered by the plant’s convex hull and the area covered by the actual plant.
Leaf Perimeter: Particularly useful for the basic leaf shape and width evaluation (combined with leaf area).
Eccentricity: Plant shape estimation, scalar number, eccentricity of the ellipse with same second moments as the plant (0…circle, 1…line segment).
Roundness: Based on evaluating the ratio between leaf area and perimeter. Gives information about leaf roundness.
Medium Leaf Width Index: Leaf area proportional to the plant skeleton (i.e. reduction of the leaf to line segment).
Circle Diameter: Diameter of a circle with the same area as the plant.
Convex Hull Area: Useful for compactness evaluation
Centroid: Center of the plant mass position (particularly useful for the eccentricity evaluation)
Number of leaves
Leaf movement – Biomass assessment
Leaf movement – Relative growth rate

Parameter Validation

Parameter measurements have been successfully validated using model objects with known shape and dimensions:

Leaf Tracking and Movement

Morphological segmentation and leaf tracking analysis is used to characterize development and architecture of individual plant leaves as they progress through development or progression of stress imposition. PlantScreen^TMSystem algorithm for leaf tracking runs over binary representations of individual plants and the time series.

Dynamic Morphometric Analysis

Progressive drought stress analysis in Arabidopsis Col-0 plants.Drought stress influenced not only biomass production but also the morphology of the plants. Other parameters e.g. compactness and perimeter were also affected.

Other Measured Parameters

Color segmentation for plant fitness evaluation
Sequentially computed relative leaf growth rates
Comparison of leaf area differences during whole experiment
Flattening index
Circadian leaf area differences
Greening index
Contribution of individual colors after color segmentation and characterization:
- Healthy Green
- Dark Green
- Light Green
- Other Color – for incidental stains

Greening index for different plants characterizing species specific pigments content in leaves. 25-hue color scale include green, yellow and red color spectra for the greening index analysis. Charts show the proportion of each hue in the corresponding plants above.