High throughput plant phenotyping for the development of better plants for the future
Matthias Eberius 路 CEO LemnaTec Head of Research and Development matthias.eberius@lemnatec.com
The challenges quantifying human vision imaging far beyond direct human vision incorporating human experience of visual evaluation in algorithms target directed development of solutions integrating biological systems and technology customising solutions for specific research needs keeping systems open for future research developments Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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LemnaTec interdisciplinary team 12 years of experience with image based biological measurement in-house development of image processing software in-house development of hardware development of comprehensive solutions
compliance with standards
Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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Hardware
3D scanalyzer accelerating plant phenomics
Accelerating plant phenomics
opening new prospects high-throughput screens multiple camera units non-destructive measurement quantitative analysis monitor growth dynamics stress assessment link to genomics
Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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scanalyzer3D Imaging cabinets Fully automated, comprehensive imaging for plant shoots and roots
Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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scanalyzer3D multiple imaging 3D imaging of full plants 1.
3.
Speaker: Matthias Eberius – CEO
2.
1. 2. 3. 4.
top View side View side View 90° more views optional
Date: 5/4/2010
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scanalyzer3D scanning modes Scanning in different wavelength and modes 1. infrared light – shoot 2. visible light – shoot 3. near infrared – root 4. near infrared light – shoot 2.
3.
4.
5.
5. fluorescent light – shoot
1. Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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scanalyzer3D IR imaging 1.
Scanning – infrared light Quantify temperature differences (e. g. within leaves and between plants)
Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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scanalyzer3D VIS imaging – shape 2.
Scanning – visible light High-resolution colour images for comprehensive morphological and growth phenotyping
Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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scanalyzer3D VIS imaging – colour 2.
Scanning – visible light Plant colour classification – Key to plant health, stress, nutrients and senecence
Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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scanalyzer3D VIS imaging – architecture 2.
Scanning – visible light Plant skeleton analysis – key to growth dynamics, morphology and architecture
Speaker: Matthias Eberius – CEO
separation of stem and leaves information about nodes, length of leaves morphology plant growth phases
Date: 5/4/2010
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scanalyzer3D NIR imaging – root 3.
Scanning – near infrared light for roots spatial distribution of water content in soil
0h 2h 4h 6h 8h Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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scanalyzer3D NIR imaging – shoot 4.
Scanning – near infrared light (NIR) measuring water distribution and dynamics
0h
4h wheat dried down over 16 h at elevated temperature
8h Speaker: Matthias Eberius – CEO
16h Date: 5/4/2010
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scanalyzer3D flourescence imaging 5.
Scanning – flourescent light blue light (< 500 nm) visualises any related fluorescence
Speaker: Matthias Eberius – CEO
Chlorophyll (cont., flash) Green fluo. Protein (GFP) Phenolics Autofluorescence Custom solutions Date: 5/4/2010
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Hardware
movingfield linking greenhouse to field
movingfield Speaker: Matthias Eberius – CEO
Automating plant handling Plant transport 1-40 kg randomisation Precision watering Multiple solution fertilising Pesticide spraying High density growth Environment monitoring Date: 5/4/2010
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movingfield – watering Speaker: Matthias Eberius – CEO
individual plant watering plant weighing target humidity watering multiple solution fertilising top or bottom watering salinity control water logging water use efficiency Date: 5/4/2010
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movingfield – spraying Speaker: Matthias Eberius – CEO
automated spraying closed cabin uniform dosage no greenhouse contamination high quality nozzles spraying at night possible air ventilation active carbon filtering optional Date: 5/4/2010
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movingfield – conveyor
high frequency imaging changing neighbours Speaker: Matthias Eberius – CEO
equilibrating hotspots (light, air humidity) Date: 5/4/2010
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movingfield â&#x20AC;&#x201C; conveyor Impressions of the movingfield
Speaker: Matthias Eberius â&#x20AC;&#x201C; CEO
Date: 5/4/2010
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movingfield – conveyor Reliable transport (700 $ per plant!) Highly modular
Size adjustable (1000…) Later changes possible/expandable Plant height up to 3m Technology taken from automotive + supplier production Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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Hardware
HTS scanalyzer small plant phenotyping
scanalyzerHTS high resolution imaging of trays and MTPs
Speaker: Matthias Eberius â&#x20AC;&#x201C; CEO
Date: 5/4/2010
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scanalyzerHTS high precision xy table
Speaker: Matthias Eberius â&#x20AC;&#x201C; CEO
Date: 5/4/2010
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scanalyzerHTS special features
Special features top or backlight NIR, cloudy day and fluorescent light options
Speaker: Matthias Eberius – CEO
trays or multiwell plates easy exchange of inlays automatic barcode identification Date: 5/4/2010
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scanalyzerHTS 3D laser scanning 3D laser scanning height of small plants leaf angle leaf movement 900 nm laser optional
Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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scanalyzerHTS imaging
High-throughput screening multiple imaging per plate/tray High precision positioning 6 to 384 well plates Up to 54 plate per run Speaker: Matthias Eberius – CEO
High magnification up to XXµm resolution Up to 96 images per plate (single well mode) Fast analysis while imaging Date: 5/4/2010
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scanalyzerHTS movement assays Analysing movement of small organisms movement quantification spatial distribution of movements movement pattern life/death classification
Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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scanalyzerHTS feeding assays HT-screening for leaf eating organisms feeding assays resistance screens (BT) organism sizes mortality assessment
Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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Hardware
PL scanalyzer low throughput, but a great deal of options
scanalyzerPL
Speaker: Matthias Eberius – CEO
top cameras (1 or 2) VIS, Fluo, NIR zoom lens systems backlight, toplight higher plants trays multiwell plates beakers with floating organisms Date: 5/4/2010
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Hardware
Cameras Specifications & resolutions
Cameras – Specifications RGB Camera sensor size 2448 x 2050 pixels (h x v pixels)
max. frame rate 17 frames per second (at full resolution) spectral sensitivity 400–700 / 950 nm with / without filter
field of application high light conditions excitation/ emission
Speaker: Matthias Eberius – CEO
Fluorescence Camera 1392 x 1040 pixels 17 frames per second 400–700 / 950 nm low light conditions 420–500 nm / > 510 nm
Date: 5/4/2010
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Cameras – Specifications NIR Camera sensor size 640 x 512 pixels (h x v pixels)
max. frame rate 30 frames per second (at full resolution)
IR Camera 320 x 240 pixels up to 40 frames per second
spectral sensitivity 900–1700 nm (NIR) with / without filter
8–14 µm (LWIR)
field of application all light conditions
-30°C to +90°C
Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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Cameras – Resolutions mm per pixel
pixel per mm
scanalyzerPL Macro (min. zoom)
0.0838
11.936
scanalyzerPL Macro (max. zoom)
0.0149
67.253
scanalyzerHTS Macro (min. zoom)
0.0838
11.936
scanalyzerHTS Macro (max. zoom)
0.0149
67.253
scanalyzerHTS Micro (min. zoom)
0.0167
59.707
scanalyzerHTS Micro (max. zoom)
0.0030
335.342
scanalyzer3D Macro (min. zoom)
0.8379
1.193
scanalyzer3D Macro (max. zoom)
0.1484
6.720
Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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Spectral sensitivity NIR-Camera
Speaker: Matthias Eberius â&#x20AC;&#x201C; CEO
Date: 5/4/2010
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Software
Software Linking data acquisition with analysis, creating and optimising data flows
Software: architecture
LemnaLauncher LemnaControl
LemnaBase
Speaker: Matthias Eberius â&#x20AC;&#x201C; CEO
LemnaGrid
LemnaControl
LemnaMiner
LemnaCount
LemnaTrack
Date: 5/4/2010
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Software
LemnaLauncher Managing all software processes
Software: LemnaLauncher Main program DB / Grid / Miner tree view snapshot view reanalyze database administration run biotest
Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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Software: LemnaLauncher
Speaker: Matthias Eberius â&#x20AC;&#x201C; CEO
Date: 5/4/2010
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Software
LemnaControl Monitoring the fully integrated automatisation of all LemnaTec scanalyzer systems
Software: LemnaControl Monitoring of all systems imaging/image analysis watering/spraying randomising plants in the greenhouse/growth chamber importing metadata from connected databases linking plants/trays/multiwell plates to specific imaging modes controlled placing of MTPs on different imaging positions (by robots) switching lights or heating on and off
Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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Software: LemnaLauncher
Speaker: Matthias Eberius â&#x20AC;&#x201C; CEO
Date: 5/4/2010
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Software
LemnaGrid Image analyzing software
Software: LemnaGrid Image analysis Drag and drop modules High flexibility Transparent data flow No programming language necessary Self assembling image analysis wizard Exclusive plugin algorithms optional Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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Software: LemnaLauncher
Speaker: Matthias Eberius â&#x20AC;&#x201C; CEO
Date: 5/4/2010
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Software: LemnaGrid – Wizard Imaging GridWizard parameterise each analysis step direct visual feedback on parameter changes general explanation of algorithm function context and grid specific comments on algorithm function Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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Software: LemnaLauncher
Speaker: Matthias Eberius â&#x20AC;&#x201C; CEO
Date: 5/4/2010
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Software
LemnaMiner The correlation software
Software: LemnaMiner Querying databases
Speaker: Matthias Eberius – CEO
easy access to database
storable queries and spreadsheets
fast graphical data survey
complex calculations based on graphical interface
direct link between images and data
transformation of raw data to biological relevant parameters
preorganisation of multi-dimensional data for statistical analysis
data formating for export Date: 5/4/2010
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Software: LemnaLauncher
Speaker: Matthias Eberius â&#x20AC;&#x201C; CEO
Date: 5/4/2010
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LemnaMiner – Data analysis grids Data analysis grids drag and drop modules high flexibility Transparent data flow no database language necessary complex calculations within snapshots and time series biological data transformation Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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Software: LemnaLauncher
Speaker: Matthias Eberius â&#x20AC;&#x201C; CEO
Date: 5/4/2010
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Software
LemnaBase Handling large datasets
Software: LemnaBase Flexible data base Linux PostgreSQL or Oracle up to 100 TB dynamic structure following result needs maximum transparency minimised access time open interface for LIMS integration Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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Software: LemnaLauncher
Speaker: Matthias Eberius â&#x20AC;&#x201C; CEO
Date: 5/4/2010
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Software
LemnaShare Connecting multiple users
Software: LemnaShare Sharing progress online exchange interface up- and download of analysis grids exchange within research projects and academia exchange between companies and phenotyping facilities support by LemnaTec avoiding double development sharing experience Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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Software: LemnaLauncher
Speaker: Matthias Eberius â&#x20AC;&#x201C; CEO
Date: 5/4/2010
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Software
LemnaCount Quantifying biological objects
Software: LemnaCount Reliable count counting high numbers assessment of size, colour, shape object classification high reproducibility
Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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Software
LemnaTrack Movement quantification software
Software: LemnaTrack Quantifying movement assessment of translational and within organism movement life/death classification spatial resolution of movement movement patterns Visualising movement Speaker: Matthias Eberius – CEO
Date: 5/4/2010
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Software: LemnaLauncher
Speaker: Matthias Eberius â&#x20AC;&#x201C; CEO
Date: 5/4/2010
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