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High throughput plant phenotyping for the development of better plants for the future
Matthias Eberius · CEO LemnaTec
Head of Research and Development
matthias.eberius@lemnatec.com
The challenges
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 13
quantifying human vision
imaging far beyond direct human vision
incorporating human experience of visual evaluationin algorithms
target directed development of solutions
integrating biological systems and technology
customising solutions for specific research needs
keeping systems open for future research developments
LemnaTec
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 14
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
scanalyzer3D
accelerating plant phenomics
Hardware
Accelerating plant phenomics
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 16
opening new prospects
high-throughput screens
multiple camera units
non-destructive measurement
quantitative analysis
monitor growth dynamics
stress assessment
link to genomics
scanalyzer3D Imaging cabinets
Slide 17Speaker: Matthias Eberius – CEO Date: 5/4/2010
Fully automated, comprehensive imaging for plant shoots and roots
scanalyzer3D multiple imaging
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 18
1. top View
2. side View
3. side View 90°
4. more views optional
3D imaging of full plants
1. 2.
3.
scanalyzer3D scanning modes
Slide 19Speaker: Matthias Eberius – CEO Date: 5/4/2010
1.
2.3.
4.5.
1. infrared light – shoot
2. visible light – shoot
3. near infrared – root
4. near infrared light – shoot
5. fluorescent light – shoot
Scanning in different wavelength and modes
scanalyzer3D IR imaging
Slide 20Speaker: Matthias Eberius – CEO Date: 5/4/2010
1. Scanning – infrared light
Quantify temperature differences (e. g. within leaves and between plants)
scanalyzer3D VIS imaging – shape
Slide 21Speaker: Matthias Eberius – CEO Date: 5/4/2010
Scanning – visible light
High-resolution colour images for comprehensive morphological and growth phenotyping
2.
scanalyzer3D VIS imaging – colour
Slide 22Speaker: Matthias Eberius – CEO Date: 5/4/2010
2. Scanning – visible light
Plant colour classification – Key to plant health, stress, nutrients and senecence
scanalyzer3D VIS imaging – architecture
Slide 23Speaker: Matthias Eberius – CEO Date: 5/4/2010
separation of stem and leaves
information about nodes, length of leaves
morphology
plant growth phases
2. Scanning – visible lightPlant skeleton analysis – key to growth dynamics, morphology and architecture
scanalyzer3D NIR imaging – root
Slide 24Speaker: Matthias Eberius – CEO Date: 5/4/2010
Scanning – near infrared light for roots
spatial distribution of water content in soil
3.
0h 2h 4h 6h 8h
scanalyzer3D NIR imaging – shoot
Slide 25Speaker: Matthias Eberius – CEO Date: 5/4/2010
Scanning – near infrared light (NIR)
measuring water distribution and dynamics
4.
0h 4h
8h 16h
wheat dried down over 16 h at elevated temperature
scanalyzer3D flourescence imaging
Slide 26Speaker: Matthias Eberius – CEO Date: 5/4/2010
Scanning – flourescent light
blue light (< 500 nm) visualises any related fluorescence
5.
Chlorophyll (cont., flash)
Green fluo. Protein (GFP)
Phenolics
Autofluorescence
Custom solutions
movingfieldlinking greenhouse to field
Hardware
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 28
movingfield
Automating plant handling
Plant transport 1-40 kg
randomisation
Precision watering
Multiple solution fertilising
Pesticide spraying
High density growth
Environment monitoring
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 29
movingfield – watering
individual plant watering
plant weighing
target humidity watering
multiple solution fertilising
top or bottom watering
salinity control
water logging
water use efficiency
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 30
movingfield – spraying
automated spraying
closed cabin
uniform dosage
no greenhouse contamination
high quality nozzles
spraying at night possible
air ventilation
active carbon filtering optional
movingfield – conveyor
Slide 31Speaker: Matthias Eberius – CEO Date: 5/4/2010
high frequency imaging
changing neighbours
equilibrating hotspots (light, air humidity)
movingfield – conveyor
Slide 32Speaker: Matthias Eberius – CEO Date: 5/4/2010
Impressions of the movingfield
movingfield – conveyor
Slide 33Speaker: Matthias Eberius – CEO Date: 5/4/2010
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
scanalyzerHTS
small plant phenotyping
Hardware
scanalyzerHTS
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 35
high resolution imaging of trays and MTPs
scanalyzerHTS
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 36
high precision xy table
scanalyzerHTS special features
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 37
Special features
top or backlight
NIR, cloudy day andfluorescent light options
trays or multiwell plates
easy exchange of inlays
automatic barcodeidentification
scanalyzerHTS 3D laser scanning
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 38
3D laser scanning
height of small plants
leaf angle
leaf movement
900 nm laser optional
scanalyzerHTS imaging
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 39
High-throughput screening
multiple imaging per plate/tray
High precision positioning
6 to 384 well plates
Up to 54 plate per run
High magnification up toXXµm resolution
Up to 96 images per plate(single well mode)
Fast analysis while imaging
scanalyzerHTS movement assays
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 40
Analysing movement of small organisms
movement quantification
spatial distribution of movements
movement pattern
life/death classification
scanalyzerHTS feeding assays
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 41
HT-screening for leaf eating organisms
feeding assays
resistance screens (BT)
organism sizes
mortality assessment
scanalyzerPL
low throughput, but a great deal of options
Hardware
scanalyzerPL
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 43
top cameras (1 or 2)
VIS, Fluo, NIR
zoom lens systems
backlight, toplight
higher plants
trays
multiwell plates
beakers with floatingorganisms
CamerasSpecifications & resolutions
Hardware
Cameras – Specifications
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 45
RGB Camera Fluorescence Camerasensor size
(h x v pixels)2448 x 2050 pixels 1392 x 1040 pixels
max. frame rate (at full resolution)
17 frames per second 17 frames per second
spectral sensitivity with / without filter
400–700 / 950 nm 400–700 / 950 nm
field of application high light conditions low light conditions
excitation/emission
420–500 nm / > 510 nm
Cameras – Specifications
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 46
NIR Camera IR Camerasensor size
(h x v pixels)640 x 512 pixels 320 x 240 pixels
max. frame rate (at full resolution)
30 frames per second up to 40 frames per second
spectral sensitivity with / without filter
900–1700 nm (NIR) 8–14 µm (LWIR)
field of application all light conditions -30°C to +90°C
Cameras – Resolutions
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 47
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
Spectral sensitivity NIR-Camera
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 48
SoftwareLinking data acquisition with analysis, creating and optimising data flows
Software
Software: architecture
Date: 5/4/2010 Slide 50Speaker: Matthias Eberius – CEO
LemnaLauncher
LemnaControl LemnaGrid LemnaMiner
LemnaBase LemnaControl LemnaCount LemnaTrack
LemnaLauncherManaging all software processes
Software
Software: LemnaLauncher
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 52
Main program
DB / Grid / Miner
tree view
snapshot view
reanalyze
databaseadministration
run biotest
Software: LemnaLauncher
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 53
LemnaControlMonitoring the fully integrated automatisationof all LemnaTec scanalyzer systems
Software
Software: LemnaControl
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 55
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
Software: LemnaLauncher
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 56
LemnaGridImage analyzing software
Software
Software: LemnaGrid
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 58
Image analysis
Drag and drop modules
High flexibility
Transparent data flow
No programming languagenecessary
Self assembling imageanalysis wizard
Exclusive pluginalgorithms optional
Software: LemnaLauncher
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 59
Software: LemnaGrid – Wizard
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 60
Imaging GridWizard
parameterise eachanalysis step
direct visual feedbackon parameter changes
general explanationof algorithm function
context and grid specificcomments on algorithmfunction
Software: LemnaLauncher
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 61
LemnaMinerThe correlation software
Software
Software: LemnaMiner
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 63
Querying databases
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 tobiological relevant parameters
preorganisation of multi-dimensional data for statistical analysis
data formating for export
Software: LemnaLauncher
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 64
LemnaMiner – Data analysis grids
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 65
Data analysis grids
drag and drop modules
high flexibility
Transparent data flow
no database languagenecessary
complex calculationswithin snapshots andtime series
biological datatransformation
Software: LemnaLauncher
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 66
LemnaBaseHandling large datasets
Software
Software: LemnaBase
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 68
Flexible data base
Linux PostgreSQLor Oracle
up to 100 TB
dynamic structure followingresult needs
maximum transparency
minimised access time
open interface for LIMS integration
Software: LemnaLauncher
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 69
LemnaShareConnecting multiple users
Software
Software: LemnaShare
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 71
Sharing progress online exchange interface up- and download of analysis
grids exchange within research
projects and academia exchange between
companies and phenotypingfacilities
support by LemnaTec avoiding double development sharing experience
Software: LemnaLauncher
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 72
LemnaCountQuantifying biological objects
Software
Software: LemnaCount
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 74
Reliable count
counting high numbers
assessment of size, colour, shape
object classification
high reproducibility
LemnaTrackMovement quantification software
Software
Software: LemnaTrack
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 76
Quantifying movement
assessment of translationaland within organismmovement
life/death classification
spatial resolution ofmovement
movement patterns
Visualising movement
Software: LemnaLauncher
Date: 5/4/2010Speaker: Matthias Eberius – CEO Slide 77
Visit our website www.lemnatec.com
Thank you for your attention!
Visit our website www.lemnatec.com
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