High throughput phenotyping are fully automated facilities in greenhouses or growth chambers with robotics, precise environmental control, and remote sensing techniques to assess plant growth and performance

1. PRESENTATION
ON
HIGH THROUGHPUT PHENOTYPING
ASHISH KUMAR TIWARI (Ph.D)
Deptt. of Genetics and Plant Breeding

2. Introduction

3. High throughput phenotyping are fully automated
facilities in greenhouses or growth chambers with
robotics, precise environmental control, and remote
sensing techniques to assess plant growth and
performance.
The Plant Accelerator’s phenotyping capacity, which is
built around the LemnaTec Scanalyzer 3D platform,
consists of four smart houses; these are fully climate-
controlled greenhouses equipped with computer-
controlled conveyor belts carrying up to 600 plants per
room.

4. • Each smart house is linked to one of two imaging
halls, within which are five imaging chambers.
Cameras in these chambers record images of
plants in a range of different wavelengths, from
far infrared through to UV-fluorescence,
providing a diversity of phenotype information.
• Visible cameras quantify overall plant
morphology, size, colour, shoot mass and other
physical characteristics, near infra-red cameras
detect water content of the leaves and soil, far
infra-red provides information about leaf
temperature and transpiration rate, and UV
lighting detects chlorophyll.

5. The various parameters are measure includes
• Leaf area,
• Leaf colour,
• Leaf angle
• Leaf rolling,
• Leaf elongation,
• Chlorophyll content,
• Stem diameter,
• Plant height/width,
• Stress pigment concentration,
• Tip burn,
• Internode length,
• Seed number,
• Seed size,
• Tiller number,
• Flowering time,
• Germination time etc.

6. Steps involved in phenotyping
• Plant phenotyping system focusing in the
different stage of the plant.
• It has the capability to image plants in a
greenhouse by automatically moving plants.
• Positioning them in front of a stereoscopic
camera.
• Proprietary software analyzes the images to
extract phenotypic-related information.

8. Scanning in different wavelength and
modes
1. Scanning by visible light (RGB)
• High-resolution colour images for comprehensive
morphological and growth phenotyping. Under reproducible
illumination conditions provide the best basis for
comprehensive phenotyping. High-resolution colour images
taken from the top and several sides.

9. 3.IR infrared light
With infrared light, high-throughput 3-D imaging systems provide a
unique chance to quantify temperature differences (e. g. within leaves and
between plants).

10. 3) Fluorescence Imaging
Chlorophyll Fluorescence
• The light energy absorbed by green plants meets one of the following three fates:
(1) One part of this energy is used for electron transport and carbon assimilation
(photochemical quenching).
(2) Another fraction of the incident light energy is dissipated as heat via the
xanthophyll cycle (non-photochemical quenching).
(3) Finally, the remainder of light energy is emitted as fluorescence.
Fv/Fm intervals during several stages of symptom development in bean plants .

11. 4.NIR / RGB
Near-infrared (NIR) cameras study water content and
movement in leaves and soil.
They use light in the NIR region of the spectrum (900–1550 μm)
Plants are grown in clear pots so
roots can be photographed while
the plant is growing.
Soil NIR measurements are used
to calculate:
• how much water the roots remove from
the soil.
• where and how much water the plant is
using.

12. • Far infrared (FIR) imaging
Cooler plants have better root systems and take up
more water.

13. Magnetic resonance imaging (MRI)
Magnetic resonance imaging (MRI) is
used to study plant roots.
• MRI uses a magnetic field and
radio waves to take images of
roots.
• MRI allows the 3D geometry
of roots to be viewed just as if
the plant was growing in the
soil.

14. Three-dimensional (3D) imaging
Digital photos of the top and sides of plants are combined into
a 3D image.
Measurements that can be taken using a 3D image include:
• shoot mass
• leaf number, shape and angle
• leaf colour
• leaf health.

15. Image Analysis software
LemnaGrid-
The image analysis grids combine efficient development in a graphic
interface with excellent surveys on image analysis.
LemnaMiner-
By correlating image analysis data with other experimental data the
results are transformed into biologically relevant information for
subsequent statistical analysis.
LemnaLauncher-
Universal interface for machine / analysis / database management of
all Scanalyzer systems.
LemnaControl-
Control center for imaging and plant / data handling, robots and
greenhouse logistics.

16. LemnaBase-
Data handling medium offering consistent and adequate
data storage of up to 20 terabyte.
LemnaShare-
Supervised exchange platform for LemnaTec image analysis
Agrids.
LemnaCount-
Image and data analysis tool for standardised counting and
measurement applications.
LemnaTrack-
Image and data analysis portfolio to identify small organism
behaviour and mobility.

17. IRGA –
Uptake of CO2 can be measured with the means of an IRGA
(Infra-Red Gas Analyzer) which can compare the CO2
concentration in gas passing into a chamber surrounding a
leaf/plant and the CO2 leaving the chamber. The first hand
held photosynthesis measuring device was launched in
1992.

18. Mini Plant Photosynthesis Meter
The new miniPPM is the third generation of our plant
photosynthesis meter. It features the latest innovations in optics
and electronics and is based on a new, advanced measuring
concept. Electronics innovation and smaller components made it
possible to design an entirely new device, much smaller and
lighter in weight than previous versions, without compromising
on quality and accuracy. Yet the instrument is simple in
operation: just press the button and a photosynthesis
measurement is completed within a second. Laboratory tests
show excellent properties. Measurements are stable and
reproducible.

19. Canopy sensor:-
Chlorophyll concentrations have been measured nondestructively
by absorbance methods. A commonly used absorbance chlorophyll
meter is the Minolta SPAD-502 meter . Monje and Bugbee (1992)
conducted an experiment in which the dual-wave SPAD-502
chlorophyll meter was tested against a custom-built single-wave meter
and then destructive colorimetric measurement was performed to find
in vitro chlorophyll concentration to compare the absorbance
measurements.

20. Infrared Thermometer-
Infrared thermometers use for monitoring evapotranspiration
rates in crops (Stone and Horton, 1974) and in the observation of daily
crop temperatures (Blad and Rosenberg, 1976). Leaf and canopy
temperatures have been fast and easy to measure with infrared
thermometers and have been related to plant water stress.

21. Application
Plant Phenotyping & Functional Genomics
Non-destructive, multispectral plant imaging and
comprehensive control of water evaporation/supply allow optimal
assessment of GxE impact on phenotypes under stress or natural
field conditions.
Breeding of new Traits
Quantitative phenotype assessment of seed
collections/crossing programmes guarantees fast data access, even
with complex traits such as drought tolerance.
High Content & High Throughput Screening
Multi-parameter assessment of a wide range of
organisms and assay types across thousands of samples provides a
reliable basis for agrochemical/pharmaceutical screening.

22. Life Science Research & Drug Discovery
Assessment of small organisms
(nematodes, fish eggs, parasites) and cell cultures
– new prospects for the screening of active
ingredients and pharmacological key structures.
Quality Control
All Scanalyzer hard- and software
modules can be customised to target most quality
control solutions in agricultural or pharmaceutical
applications.

23. • Advantages-
• Interconnected breeding and trait validation process.
• The development of information and data storage technologies,
providing suitable tools for the analysis of complex structures of
plants.
• The need to accelerate breeding.
• The impossibility for individual breeders and senior research experts
to acquire all important data themselves, in order to keep in control of
subjectivity effects.
• To quantify more complex traits.
• The necessity to spot increasingly smaller differences.
• Disadvantages
• High developmental cost.
• For Image analysis and data interpretation well trained person required.