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life science research high-throughput screening plant functional genomics ecotoxicology high-content screening
ing > Field Phenotyp rescence – o u fl n o ti lu o s re > High activity II S P r fo m F / v F imaging l a tr c e p rs e p y H >
cell analysis colony counting drug discovery quality control
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The challenges LemnaTec’s ambition is to reproducibly quantify human vision on organisms. Therefore the LemnaTec scan alyzer platform generates digital images in a wide range of wavelengths – far beyond human vision. The LemnaTec software automatically analyses these images, resulting in a Dipl. Biol. Dirk Vandenhirtz CEO
considerable number of quantitative visual parameters. LemnaTec develops imaging and automated plant management as well as plant treatment systems, image
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analysis and data handling modules and also strategies to meet the needs of today’s research and industry. We enable customers to
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design and develop products suitable for future challenges.
The targets LemnaTec’s team of scientists develops
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join the mission
hard- and software solutions for highthroughput and high-content screening of plants, seedlings, insects and other organisms and for the automated evaluation of bio tests in ecotoxicology. Digital images are primarily taken by the scanalyzer systems PL, HTS, Field and 3D, all set up in a modular design. Using advanced LemnaTec image processing algorithms, every visible sample parameter (e. g. colour, shape, size, architecture) is subsequently measured and correlated with experimental records (e. g. genetic data). Our aim: to visualise and analyse the biology beyond human vision.
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The tools – hardware
The tools – software
scanalyzer3D manual loaded imaging units with top and side imaging capabilities for 3D plant phenotyping
LemnaLauncher universal interface for machine/analysis/database management of all scanalyzer systems
scanalyzer3D HT automatic imaging and transport of plants in greenhouses and growth chambers, combined with watering and spraying systems, providing standardised growth conditions and non-destructive daily measurements
LemnaControl control center for imaging and plant/data handling, robots and greenhouse or growth chamber logistics
scanalyzerfield a wide range of choices for the quantitative, nondestructive analysis of different crops or model plants in field conditions scanalyzerHTS high-throughput, high-content screening for agricultural, phenotypical and pharmaceutical purposes scanalyzerPL the basic system for all quantitative biological imaging – from ecotoxicology and small plant analysis to colony counting and seed analysis
LemnaGrid highly flexible image analysis development kit for advanced imaging tasks LemnaMiner data mining and data correlation tool to generate biologically relevant information LemnaBase data handling medium offering consistent and adequate data storage of up to 100 terabyte LemnaShare supervised exchange platform for LemnaTec image analysis grids
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Accelerating plant phenomics LemnaTec scanalyzer3D systems open new prospects for the quantitative, non-destructive analysis of different crops or model plants under high-throughput conditions. Each plant is imaged sequentially in multiple scanalyzer3D camera units, employing different wavelengths that reach far beyond human vision. The result is an unprecedented number of reproducible and significant data points on any aspect of plant development. Data will be collected continuously and recorded in one snapshot per run through the
scanalyzer
3D
Âscanalyzer3D, thus routinely producing 15 or more images and several hundred data points per plant and run. Plants are imaged in multiple runs throughout their entire life cycle. All data is available in the database within minutes of imaging – for unparalleled monitoring of dynamic plant development. Comprehensive quantitative representation of plants in datasets generates special data for physiological and genetic plant modeling to identify and quantify the concealed parameters that really control plant development. Such deep insights into plant biology accelerate phenomics and enable plant breeding to deal with the challenges of the 21st century by measuring dynamic data in relatively early stages of plant growth.
1.
Scanning – 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).
2.
3.
4.
1. 2.
Scanning – visible light
High-resolution colour images taken from the top and several sides under reproducible illumination conditions provide the best basis for comprehensive phenotyping.
3.
Scanning – near infrared light for roots
Humidity visualisation in root columns by near infrared light provides added information on spatial root performances of plants under high-throughput conditions.
4.
Scanning – near infrared light
Visualisation of water distribution and dynamics (1450-1550 nm) as well as further NIR-absorbing ingredients.
5.
Scanning – fluorescent light
Using blue light large field excitation (< 500 nm) in back/top light conditions visualises any related fluorescence between 520 and 750 nm (GFP, phenolics, etc).
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5.
Fv/Fm for PSII activity
Photosynthesis Fluorescent Imaging LemnaTec is pleased to announce the release of its new highthroughput imaging technology for physiologically related measurements of photosynthesis. The measurement principle is based on imaging the Kautsky induction or fast chlorophyll fluorescence induction curve of photosynthesis using one high intensity light pulse for 1 – 3 s.
control
drought stressed
Unlike some other technologies, LemnaTec is able to provide a technology solution that combines fast and efficient high-throughput screening of photosynthetic activity with flexibility to offer: n
Whole plants of different sizes imaged remotely and yielding low noise at high resolution images
n
dark adapted: no significant effect
Dark and light adapted plant measurements protocols including adaption tunnels
n
Measurements tolerant to leaf angle for side and top imaging in high throughput applications
n
LED flash ranging up to 5000 µmol/m²s to measure even under high light adaptation
light adapted: significant effect
Hyperspectral imaging is a technology widely used for remote imaging, in an effort to extract a maximum of information out of images made under strongly varying imaging conditions, caused by the variability of the sunlight and changing atmospheric conditions.
Hyperspec= High Spectral and Spatial Resolution one pixel
=
n
1 spatial pixel measured at up to 930 wavelengths
n
Each Pixel contains a continous spectrum that is
Image [Y]
used to identify the condition of the plant or fruit Image
[X]
n -1 Wavenumber [cm ]
Multi-Disciplinary Research Applications n
State of the art camera
n
Retrofit to all existing scanalyzer3D and scanalyzer HTS possible
n
Optimised for visible and near infrared applications
E.g.: Optimised spectral detail in Chlorophyll red band for more accurate classifications
hyperspec imaging
Hyperspec Imaging
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9 8 7 6 5 11380
4
5830 1702
5992
scanalyzer
3D HT
Enhancing the statistical power of greenhouse and growth room trials
15 14 13 12 11 10
LemnaTec scanalyzer3D HT systems open new prospects for the quantitative, nondestructive analysis of different crops or model plants under high-throughput conditions. Each plant is transported automatically to multiple scanalyzer3D imaging units using high quality conveyor belt systems. The result is an unprecedented number of reproducible and significant data points on any aspect of plant development without any human interaction required. LemnaTec’s high denng Scale and wateri station
sity plant carrier system also provides options to equip growth rooms with scanalyzer3D HT systems to achieve full control of environmental conditions and significantly reduced experimental variability.
Watering and weighing systems The LemnaTec plant conveyor system includes the provision of high-precision Spray station
and controlled watering – it is geared to each individual plant’s requirements (watering based on pot weight which is related to soil moisture) allowing researchers to impose many kinds of saline stress or drought stress regime.
Spraying cabinets LemnaTec’s comprehensive approach to plant management with its conveyor system includes further options including spray cabinets for pest management
or growth chamber. Special spray tables for manual spraying allows even plant
Foot pedale
tem minimise spreading of the active ingredients within the whole greenhouse
station
with commercial pesticides where low-drift nozzles and an efficent exhaust sys-
specific treatment with pesticides or test solutions avoiding cross contamination to other plants (e. g. non-treatment controls). Page 9
scanalyzer field – Phenotype your crops under field conditions Field phenotyping is the classical strategy to assess qualitatively and quantitatively
scanalyzer
field
agronomical important traits for field-grown plants. Many assessment methods are based on direct visual assessment or the manual use of portable measurement units. Considering the increasing amount of non-destructive, image-based measurement systems that have become available in the last few years, the scanalyzerfield provides the new option to acquire a wide range of image based data both with spatial and temporal resolution quantifying how large numbers of plants react individually on the highly dynamic environmental conditions in the field.
Precision Robotics – Imaging sensors include: n
Visible light
n
Multispectral imaging
n
Near infrared (water imaging)
n
Fluorescence
n
Infrared (heat imaging)
n
Laser height profiling
Multi-Disciplinary Research Applications Designed for non-destructive digital phenotyping in rain-out shelters, lysimeter systems and small plot phenotyping, the scanalyzerfield offers superb precision, accuracy, resolution and predictive capabilities for research in: n
Small plots for prebreeding
n
Growth assessment
n
Development of fine-tuned crop models
n
Crop physiology
n
Highly dynamic plant stress testing
n
Climate change
such as drought stress
n
Water use efficiency, soil water
n
High resolution phenotyping as reference for remote sensing
content, waterlogging n
QTL analysis
Quality Engineering for field conditions Hence, the scanalyzerfield has the following features allowing digital phenotyping of a multitude of crops, small trees and plants in specialized containers: n n
Width up to 10 m
n
Durable construction Minimised shading effects Reproducible 3D positioning for
Length up to 40 m
n
n
Height up to 6 m
n
n
Other custom sizes are also available
cameras, scanners and sensors.
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Small plant phenotyping The scanalyzerHTS is the best option for the analysis of small plants in multiwell plates or trays in specific growth chambers. The closed cabinet – containing backlight/direct or diffuse top light illumination as well as fluorescent imaging with blue light excitation – guarantees reproducible imaging conditions for all camera types provided by LemnaTec (VIS, NIR, IR, and Fluorescence). Positioning can be easily exchanged to accommodate varying plant containers and illumination types. Zoom lens systems allow imaging of fully grown Arabidopsis rosettes or complete multiwell plates/6 wells of a 96-well plate. Precise camera movement and automated tray identification by barcode enable the reliable identification of individual plants.
3-D laser scans provide further information about plant height profiles. While the scanalyzerHTS is designed as a measurement instrument,
scanalyzer
HTS
customised solutions may be placed in growth chambers.
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High content & high throughput: screening for basic research, pharmaceutical trials and plant protection
scanalyzerHTS â&#x20AC;&#x201C; high-throughput screening in perfection The LemnaTec scanalyzerHTS is the preferred platform for highthroughput screening of leaf disk assays, fungi, insects or small aquatic/terrestrial organisms such as mosquito larvae or nematodes of fish embryos. All four LemnaTec camera systems (Visible, Fluorescence, Infrared, Near Infrared) and height scanning can be applied to achieve even more detailed, single-well scanning for high-resolution growth analysis. Depending on the number and type of samples the cameras move over an array of up to 84 multiwell plates, achieving an assessment of up to 8064 different samples in one run. Additionally available robots store plates or place them in different functional locations.
isms. The observation time for each well ranges from seconds to minutes, depending on organism velocity. Movement patterns and the localisation/intensity of the movement can be quantified. Repeated measurement runs allow quantification of movement development over time, which is particularly useful for fast developing organisms (fish embryos). In all cases static image information is combined with movement information to assign movement patterns to single organisms.
scanalyzer
scanalyzerHTS provides unique opportunities to simultaneously observe large numbers of small moving organ-
HTS
Analysing movement of small organisms
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scanalyzer
PL
Low throughput, but â&#x20AC;&#x2030; a great deal of options For all low-throughput applications with manual sample exchange, the scanalyzerPL combines compact design and reproducible imaging techniques with the comprehensive control of the LemnaÂLauncher software. Test containers may range from beakers for ecotoxicity to trays with plants, smaller plants in pots or even highly reflecting fruits. Depending on the test purpose, different camera types with specific illumination systems can be mounted. The benchtop platform is available with different back and top light modules.
Camera Specifications Sensor Size
Sensitivity
VIS Camera
2448 x 2050 pixels
380 – 740 nm
Vis (High Res.) Camera
6576 x 3484 pixels
380 – 740 nm
Flu-GFP Camera
1392 x 1040 pixels
510 – 740 nm
Flu-PSII Camera
1388 x 964 pixels
680 – 900 nm
NIR Camera
640 x 512 pixels
900 – 1700 nm
IR Camera
320 x 240 pixels
8 – 14 µm
2560 x 2160 pixels
VIS, NIR
Hyperspec Camera
Spectral sensitivity NIR-Camera
camera specifications
LemnaTec scanning – The optimum in automated biological imaging
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software architecture
linking data acquisition with analysis, creating and optimising
LemnaLauncher
LemnaControl
LemnaBase
LemnaLauncher to all LemnaTec software products across the entire product range. All research
LemnaControl
images, analysis results and meta data are accessible within LemnaLauncher
Monitoring the fully integrated automati-
and are specific for the individuals product configuration and image analysis
sation of all LemnaTec scanalyzer systems
This comprehensive and intuitive interface is the main framework granting access
settings. This provides complete data management and ultimately a measure of quality assurance. Integration of all software modules provides a complete
LemnaControl is the tool to regulate and moni-
digital phenotyping workflow â&#x20AC;&#x201C; from data acquisition to image analysis to sta-
tor all appropriate system components includ-
tistical result presentation in LemnaMiner. Additionally, continuous processes
ing cameras, conveyors, robotics, illumination
accelerates result generation and analysis without human input, guaranteeing
and thus enable trained users, with or without
maximum data integrity.
any technical background to use the system. LemnaControl enables the user to initiate an experimental run on the LemnaTec scanalyzer rapidly and easily. An experimental run produces all data including images, watering, weight information and stores them into the database.
data flows
LemnaVision
LemnaLauncher
LemnaBase
LemnaVision
Convenient data storage
Supervise the system
and backup solutions
from anywhere
The core database structure based on Oracle or
To supervise the LemnaTec scanalyzer Platforms
Linux PostgreSQL technology can handle data-
remotely from outside the greenhouse or the
sets of up to 100 TB. The open interface allows
growth room, dedicated power over Ethernet
direct integration into any LIMS environment.
camera solutions can be used in combination
Combining a minimum of access time and a
with LemnaVision. LemnaVision enables the
maximum of transparency, LemnaBase ensures
user to watch and record multiple live streams
the quality and lasting value of all acquired
at the same time on different PCs, iPhones/
data and related parameters.
iPads or on dedicated displays in public areas.
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LemnaMiner
LemnaGrid
analysis network and accelerate image processing
LemnaShare
LemnaGrid Image Processing without programming knowledge LemnaGrid is the image analysis tool to address the specific needs in phenotyping with a maximum amount of flexibility. The image analysis is graphically represented as a process chain and can be subsequently saved as a
software
LemnaTec image analysis grid. Once the chain is complete it can be used to automatically analyze all images of an experiment in the background.
LemnaMiner
LemnaShare
LemnaMiner
Exchange knowledge with
Data extraction with a
users worldwide
user friendly interface LemnaMiner
LemnaGrid image analysis grids can be
The LemnaMiner software module
supplied online, as well as shared and
enables the researcher to display,
exchanged, by using the LemnaGrid ex-
filter and export resulting data from
change interface. The incoming grids,
LemnaGrid to correlate it with other
transferred to LemnaShare by the users,
experimental data and transform it
are validated and classified by LemnaTec
into biological relavant information. To
to be used by all customers as a basis
ensure data integrity within the data-
for their own work or other ready-to-use
base, LemnaMiner saves a local copy
solutions. Thus the risk of double devel-
of the queried results in a SQLite File
opments is minimised and the ongoing
on the workstation.
LemnaMiner
process of extracting increasingly relevant biological data from images can be accelerated.
LemnaGrid
LemnaShare
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applications
get phenotyping up to speed
Application examples for the scanalyzer image analysis The highly flexible and easily customisable software framework covers a wide range of applications.
Plant phenotyping & functional genomics Non-destructive, multispectral plant imaging and comprehensive control of water
Colony counting & cell analysis
evaporation/supply allow optimal assessment of GxE impact on phenotypes under
Colony counting and automatic documentation is
stress or natural field conditions.
getting increasingly important for food, beverage
Breeding of new traits
and pharmaceutical products.
Quantitative phenotype assessment of seed collections/crossing programmes guaran-
Ecotoxicology
tees fast data access, even with complex traits such as drought tolerance.
LemnaTec provides comprehensive imaging solu-
High-content & high-throughput screening Multi-parameter assessment of a wide range of organisms and assay types across thou-
tions for standardised and research tests (duckweed, daphnids, nematodes), thus maximising the quality of test results.
sands of samples provides a reliable basis for agrochemical/pharmaceutical screening.
Life science research & drug discovery
Quality control All scanalyzer hard- and software modules can be
Assessment of small organisms (nematodes, fish eggs, parasites) and cell cultures â&#x20AC;&#x201C; new
customised to target most quality control solutions
prospects for the screening of active ingredients and pharmacological key structures.
in agricultural or pharmaceutical applications.
Correlation to manual measurement
Pixel Count
Growth Plot 80 000 70 000 60 000
FAAA02
FCAA02
FHAA01
FBAA04
FEAA03
FJAA03
50 000 40 000
The Lemnatec scanalyzer systems provide
30 000
powerful predictive capabilities that are
20 000
strongly correlated to manual measure-
10 000
ments but enable research to do high
0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .03 2.03 3.03 4.03 5.03 6.03 7.03 8.03 9.03 0.03 1.03 4.04 5.04 6.04 7.04 8.04 9.04 0.04 1.04 2.04 4.04 5.04 6.04 7.04 8.04 9.04 0.04 1.04 2.04 3.04 4.04 5.04 6.04 2 2 2 2 2 2 2 2 3 3 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2
throughput screening for thousands of
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Day after sowing
assays. measure-
ments like fresh weight, size or number of leaves to digital phenotyping parameters correlations of up to 95 % can be
Correlation Study Object Length
When comparing traditional
2500 2000 1500
established. Appropriate data analysis and data modeling can help to establish correlations between growth rates and
1000 500
field yield of up to 75 % within the first 5 weeks.
0
0
20
40
60
80
100
120
140
160
180
200
Plant Height [cm]
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Concept & Design by www.v-werk.de
www.lemnatec.com LemnaTec GmbH Pascalstr. 59 52076 Aachen Germany
Web: www.lemnatec.com Mail: info@lemnatec.com Tel.: +49 (0) 24 08 / 93 83-0 Fax: +49 (0) 24 08 / 93 83-100