Upload
lemnatec
View
224
Download
2
Tags:
Embed Size (px)
DESCRIPTION
Plant Phenotyping and Plant Phenomics by LemnaTec
Citation preview
High-throughput Plant Phenotyping
a Boost for Genomics in the 21st Century
Dr. Jrg Vandenhirtz CMO LemnaTec Head of Research and Development [email protected]
LemnaTec
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 2
founded May 1998 in Aachen, Germany
interdisciplinary team (biology, physics, engineering)
12 years of experience with image based biological measurement
in-house development of image processing software
in-house development of hardware
development of comprehensive and integrated solutions
compliance with international standards
The challenges
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 3
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
The human eye
How many legs does this elephant have?
The human eye
Count the number of black dots
The human eye
are exactly the same size
The circles in the centers
The human eye
scanalyzer3D accelerating plant phenomics
Hardware
Hardware scanalyzer3D
Accelerating plant phenomics
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 10
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
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 11
Fully automated, comprehensive imaging for plant shoots and roots
scanalyzer3D multiple imaging
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 12
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
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 13
1.
2. 3.
4. 5.
1. RGB visible light
2. NIR near infrared light
3. FLUOR fluorescent light
4. IR infrared light
5. NIR near infrared root
Scanning in different wavelength and modes
scanalyzer3D VIS imaging shape
Scanning visible light
High-resolution colour images for comprehensive morphological and growth phenotyping
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 14
1.
scanalyzer3D VIS imaging colour
Scanning visible light
Plant colour classification Key to plant health, stress, nutrients and senescence
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 15
infrared light
visible light
near infrared light for roots
near infrared light
fluorescent light
1.
Scanning visible light
Plant skeleton analysis key to growth dynamics, morphology and architecture
scanalyzer3D VIS imaging architecture
separation of stem and leaves
information about nodes, length of leaves
morphology
plant growth phases
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 16
1.
scanalyzer3D VIS imaging architecture
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 17
2.
Scanning visible light Phenotyping of growth under field-density growth conditions
Phenotyping based on complex morphological criteria like: structure orientation, momentum of inertia, height, width, roundness, compactness. 0,00
0,50
1,00
1,50
2,00
2,50
3,00
3,50
4,00
4,50
0,00 1,00 2,00 3,00 4,00
axis momentum ratio
bendin
g index
medium heigt, wide,
kinked leaves
high,straight upright
compact straight,
intermediate height
compact curved
1.
scanalyzer3D NIR imaging shoot
Scanning near infrared light (NIR) measuring water distribution and dynamics
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 18
wheat dried down over 16 h at elevated temperature
2.
0h
8h
4h
16h
scanalyzer3D NIR imaging shoot
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 19
2. 0 h 4 h 8 h 16 h
wheat dried down over 16 h at elevated temperature LemnaTec NIR imaging and analysis can cover the whole water dynamics of the drying for wheat LemnaTec NIR cameras are suitable for detection of fine cereals structures of fully grown wheat
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
% N
IR a
bso
rptio
n c
lass
hours
scanalyzer3D NIR imaging shoot
Scanning near infrared light
0 h
4 h
12 h
24 h
36 h
48 h
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 20
2.
Iceberg lettuce highest water content dries out the slowest
Oak leaf lettuce green Oak leaf lettuce red red one dries out faster than green one immediate reactions already in first hour measurable
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
0 4 8 12162024283236404448
% N
IR a
bso
rptio
n cl
ass
hours
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
0 4 8 12 16 20 24 28 32 36 40 44 48
% N
IR a
bso
rptio
n c
lass
hours
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
0 4 8 12 16 20 24 28 32 36 40 44 48
% N
IR a
bso
rptio
n c
lass
hours
scanalyzer3D flourescence imaging
Scanning flourescent light blue light (< 500 nm) visualises any related fluorescence
chlorophyll (cont., flash)
green fluo. Protein (GFP)
phenolics
autofluorescence
custom solutions
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 21
3.
scanalyzer3D flourescence imaging
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 22
Visual and chlorophyl scan of a half boiled leaf
scanalyzer3D IR imaging
Scanning infrared light Quantify temperature differences
(e. g. within leaves and between plants)
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 23
4.
scanalyzer3D IR imaging
Scanning infrared light Quantify temperature differences
(e. g. within leaves and between plants)
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 24
4.
scanalyzer3D NIR imaging root
Scanning near infrared light for roots spatial distribution of water content in soil
0h 2h 4h 6h 8h
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 25
5.
scanalyzer3D NIR imaging root
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 26
Corn plant previously shown was grown in a transparent 8 cm polyacryl column Results of NIR monitoring allow measurement of spatial distribution water content in soil
0h 2h 4h 6h 8h 0
500
1000
1500
2000
0 h 2 h 4 h 6 h 8 hare
a c
las
sif
ica
tio
n p
ixe
l
total development of drying over time
0 25 50 75 100 125 150 175
L01K01J01I01
H01G01F01E01D01C01B01A01
area classified pixels
drying dynamics based on soil layer
0 h 8 h
0 25 50 75 100 125 150 175
L01
K01
J01
I01
H01
G01
F01
E01
D01
C01
B01
A01
area classified pixels
scanalyzer3D RGB imaging root
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 27
Static root density profiles growth pattern
Bangui Sweet Corn Prelude Bangui
scanalyzer3D RGB imaging root
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 28
Dynamic root growth - pattern Day 0 12 25 35 60 100
image and data show the development of roots of one plant in time.
movingfield linking greenhouse to field
Hardware
movingfield
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 30
automating plant handling
plant transport 1-40 kg
randomisation
precision watering
multiple solution fertilising
pesticide spraying
high density growth
environment monitoring
movingfield watering
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 31
individual plant watering
plant weighing
target humidity watering
multiple solution fertilising
top or bottom watering
salinity control
water logging
water use efficiency
movingfield spraying
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 32
automated spraying
closed cabin
uniform dosage
no greenhouse contamination
high quality nozzles
spraying at night possible
air ventilation
active carbon filtering optional
movingfield conveyor
high frequency imaging
changing neighbours
equilibrating hotspots (light, air humidity)
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 33
movingfield conveyor
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 34
Impressions of the movingfield
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
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 35
movingfield conveyor 1 kg
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 36
movingfield conveyor 30 kg
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 37
movingfield conveyor 30 kg
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 38
Finding the needle in the haystack
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 39
The LemnaTec Scanalyzer System discovers THE ONE which is relevant
For example, THE plant with 3% increase in value is worth $50m if it obtains 10% market penetration and released 2 years earlier
Automatic screening 10x more efficient than human screening
+3%
Modern breeding or GMO methods are able to produce THOUSANDS of new varieties per week
Phenotyping global view
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 40
Customer Status Capacity Sector relative
ACPFG Adelaide Australia (up an running) 2400 Public 17,93%
INRA Montpelier France (Finish mid 2010) 1400 Public 10,46%
INRA Dijon France (Finish end 2010) 1482 Public 11,07%
IPK I Germany Phytochamber (up and running) 600 Public 4,48%
IPK II Germany Corn (Finish mid 2010) 600 Public 4,48%
IPK II Germany Wheat (since 2008) 600 Public 4,48%
Agrobios Itally (since 2009) 500 Public 3,74%
Keygene Netherlands (Since 2008) 600 Private 4,48%
BASF USA (Since 2006) 800 Private 5,98%
Pioneer / Dupont USA (Since 2005) 1500 Private 11,21%
BASF Germany (Since 2006) 300 Private 2,24%
IGER UK (Finished 2010-2011) 800 Public 5,98%
Bayer Cropscience Belgium (Finished mid 2010) 600 Private 4,48%
Bayer Cropscience Germany (Finished end 2010) 1200 Private 8,97%
13382 100,00%
Phenotyping global view
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 41
63%
37%
Public Private
Phenotyping global view
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 42
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
USA Canada Europe China India Australia South
Amerika
Planned
Up an running
Australian Plant Phenomics Facility The Plant Accelerator
Mark Tester
ACPFG
The Plant Accelerator
The Plant AcceleratorTM
High throughput phenotyping of plant populations
4,485 m2 building, 2,340 m2 of greenhouses, 250 m2 for growth chambers
Grow >100,000 plants annually in a range of conditions
4 x 140 m2 fully automated Smarthouses
Plants delivered on 1.2 km of conveyors to five sets of cameras
High capacity state-of-the-art image capture and analysis equipment
Regular, non-destructive measurements of growth, development, physiology
First public sector facility of this type and scale in the world
Owned by University of Adelaide, opened 29 Jan 2010
National facility to support Australian plant research
Full GM and quarantine status
UniSA and ACPFG established a Chair and Assoc Prof in Plant Phenomics and Bioinformatics ($1.5m)
Growth measurements counting pixels
0
50000
100000
150000
200000
250000
300000
0 5 10 15 20 25 30 35
Proj
ecte
d sh
oot
area
[pi
xel]
Time post transplant [days]
Berkut Krichauff
meanSE;n=8
Estimation of shoot biomass
The projected shoot area of the RBG images gives a good correlation with shoot biomass
Tested for various plant species wheat, barley
rice
cotton
Arabidopsis
y = 154154x + 19065
R = 0.9205
0
50000
100000
150000
200000
250000
300000
0 0,5 1 1,5
Proj
ecte
d sh
oot
area
[pi
xel]
Dry weight [g]
5wk old barley plants, 8 cultivars
Estimation of shoot biomass
y = 216363x
R = 0,9493
y = 167807x
R = 0,9649
0
10000
20000
30000
40000
50000
60000
0 0,05 0,1 0,15 0,2 0,25
proj
ecte
d sh
oot
area
[pi
xel]
Dry weight [g]
control NaCl
20d old barley
But control and salt stressed plants have different area-weight ratios
Measured shoot dry weight [g]
Pred
icte
d sh
oot
dry
wei
ght
[g]
Golzarian et al. (2010) IEEE Proceedings Signal Processing, in review
Estimation of shoot biomass
Improved estimate of biomass when age of the plant is taken into account
Y = a0 + a1(G+B+Y)+ a2(G+B+Y)H
(H = number of days after seed preparation date)
(Correction for leaf colour did not greatly improve weight estimates)
(Cross validation run 10x)
scanalyzerHTS
small plant phenotyping
Hardware
Hardware scanalyzerHTS
scanalyzerHTS
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 56
high resolution imaging of trays and MTPs
scanalyzerHTS
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 57
high precision xy table
scanalyzerHTS special features
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 58
Special features
top or backlight
NIR, cloudy day and fluorescent light options
trays or multiwell plates
easy exchange of inlays
automatic barcode identification
scanalyzerHTS imaging
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 59
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 to 3 m per pixel tech. resolution
up to 96 images per plate (single well mode)
fast analysis while imaging
scanalyzerHTS plant assays
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 60
Arabidopsis
scanalyzerHTS plant assays
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 61
Arabidopsis
identified
scanalyzerHTS plant assays
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 62
Arabidopsis
identified
analysis
scanalyzerHTS plant assays
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 63
Image processing provides reliable quantitative
data allowing e. g. any kind of statistics and a
calculation of mean values and significances.
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
A01 A02 A03 A04 B01 B02 B03 B04 C01 C02 C03 C04 D01 D02 D03 D04
are
a
But information describing
growth remains limited.
scanalyzerHTS plant assays
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 64
t=0d t=4d t=7d t=11d
LemnaTecs image processing allows
highly automated imaging in time series.
But area based growth curves only show
a minor part of the imformation available.
How homogeneous was growth? 0
1000
2000
3000
4000
5000
6000
7000
8000
9000
0 2 4 6 8 10 12
time days
are
a leaves
A01
A02
A03
A04
B01
B02
B03
B04
C01
C02
C03
C04
D01
D02
D03
D04
scanalyzerHTS plant assays
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 65
t=0d t=4d t=7d t=11d
The slope of the curves displaying
growth rates show that most plants
grew at a relatively constant rate but
just started at different sizes e. g.
due to delay in germination.
10
100
1000
10000
0 2 4 6 8 10 12
time days
are
a leaves
A01
A02
A03
A04
B01
B02
B03
B04
C01
C02
C03
C04
D01
D02
D03
D04
scanalyzerHTS plant assays
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 66
Morphological assessment - compactness -
compactness is calculated based on the
size independent rotational momentum
of the plant
it describes if the leaves are nearer
around the centroid or farther outside
e. g. showing longer stipes
0
0,1
0,2
0,3
0,4
0,5
0,6
0 20.000 40.000 60.000 80.000 100.000 120.000
area
co
mp
actn
ess
A01
A02
A03
A04
A05
B01
B02
B04
B05
scanalyzerHTS plant assays
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 67
Morphological assessment - rotational symmetry -
rotational symmetry is calculated based
on the size independent 2nd moment
principal axis ratio
it describes in how far the leaves
alltogether show a symmetric plant
this may lead to completely other
grouping than before-mentioned
compactness
0
2
4
6
8
10
12
14
16
18
20
0 20.000 40.000 60.000 80.000 100.000 120.000
area
sym
metr
y
A01
A02
A03
A04
A05
B01
B02
B04
B05
scanalyzerHTS plant assays
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 68
Morphological assessment - excentricty -
while calculated with a different
algorithm excentricity provides here
quite similar grouping results as
rotational symmetry
nevertheless plant A02 shows more
significant distance to A01 and A03
than with rotational symmetry
0
0,1
0,2
0,3
0,4
0,5
0,6
0,7
0,8
0,9
0 20.000 40.000 60.000 80.000 100.000 120.000
area
excen
tric
ity
A01
A02
A03
A04
A05
B01
B02
B04
B05
scanalyzerHTS plant assays
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 69
Morphological assessment - medium leaf width index -
0
0,2
0,4
0,6
0,8
1
1,2
0 20.000 40.000 60.000 80.000 100.000 120.000
area
med
ium
leaf
wid
th in
dex A01
A02
A03
A04
A05
B01
B02
B04
B05
the medium leaf width index is calculated
from the square length of the plant skeleton
divided by the leaf area
it describes size independent differences in
leaf width integrating stipes, leaves and
overlapping effects.
scanalyzerHTS plant assays
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 70
Morphological assessment - area/circumference -
while having some size dependency
left the ratio of leaf area divided by
plant circumfence may allow additional
classification of morphological traits.
as with many parameters each one
provides new aspects for grouping
plants which may be especially suitable
for statistical QTL analysis
0
5
10
15
20
25
30
35
40
45
50
0 20.000 40.000 60.000 80.000 100.000 120.000
area
are
a / c
ircu
mfe
nce
A01
A02
A03
A04
A05
B01
B02
B04
B05
scanalyzerHTS plant assays
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 71
Morphological assessment - surface coverage -
surface coverage compares the
measured plant area to the area of a
circle covering the whole plant
this parameter is intended to provide a
calculation how dense the plant covers
the soil in its immediate growth area
0
0,1
0,2
0,3
0,4
0,5
0,6
0,7
0,8
0 20.000 40.000 60.000 80.000 100.000 120.000
area
su
rcace c
overa
ge m
ax c
ircle A01
A02
A03
A04
A05
B01
B02
B04
B05
scanalyzerHTS plant assays
Date: 11/10/2010
Speaker: Jrg Vandenhirtz CMO Slide 72
Morphological assessment - stockiness -
stockiness is mathematically the
description of roundness.
applied to Arabidopsis images it
separates plants with invisible or
relatively short broad stipes from
plants with long small stipes
0
20
40
60
80
100
120
140
160
0 20.000 40.000 60.000 80.000 100.000 120.000
area
sto
ckin
ess
A01
A02
A03
A04
A05
B01
B02
B04
B05
scanalyzerHTS 3D laser scanning
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 73
3D laser scanning
height of small plants
leaf angle
leaf movement
900 nm laser optional
scanalyzerHTS 3D laser scanning
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 74
Max field of view 810 mm
Max field of view in height 400 mm
Resolution in height 0.2 mm
Only in combination With HTS Scanalyzer
scanalyzerHTS 3D laser scanning
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 75
Max field of view 810 mm
Max field of view in height 400 mm
Resolution in height 0.2 mm
scanalyzerHTS movement assays
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 76
Analysing movement of small organisms
movement quantification
spatial distribution of movements
movement pattern
life/death classification
scanalyzerHTS feeding assays
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 77
HT-screening for leaf eating organisms
feeding assays
resistance screens (e. g. BT)
organism sizes
mortality assessment
scanalyzerPL
low throughput, but a great deal of options
Hardware
scanalyzerPL
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 79
top cameras (1 or 2)
VIS, Fluo, NIR
zoom lens systems
backlight, toplight
higher plants
trays
multiwell plates
beakers with floating organisms
Cameras
Specifications & resolutions
Hardware
Cameras Specifications
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 81
RGB Camera Fluorescence Camera sensor 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
400700/950 nm 400700/950 nm
field of application high light conditions low light conditions
excitation/ emission
420500 nm / > 510 nm
Cameras Specifications
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 82
NIR Camera IR Camera sensor 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
9001700 nm (NIR) 814 m (LWIR)
field of application all light conditions -30C to +90C
Cameras Resolutions
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 83
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: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 84
Software
Linking data acquisition with analysis, creating and optimising data flows
Software
Software: architecture
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 86
linking data acquisition with analysis, creating and optimising data flows
LemnaLauncher
LemnaControl LemnaGrid LemnaMiner
LemnaBase LemnaShare LemnaCount LemnaTrack
LemnaLauncher
Managing all software processes
Software
Software: LemnaLauncher
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 88
Main program
DB / Grid / Miner
tree view
snapshot view
reanalyze
database administration
run biotest
LemnaControl
Monitoring the fully integrated automatisation of all LemnaTec scanalyzer systems
Software
Software: LemnaControl
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 90
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
LemnaGrid
Image analyzing software
Software
Software: LemnaGrid
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 92
Image analysis
drag and drop modules
high flexibility
transparent data flow
no programming language necessary
self assembling image analysis wizard
exclusive plugin algorithms optional
Software: LemnaGrid Wizard
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 93
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
LemnaMiner
The correlation software
Software
Software: LemnaMiner
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 95
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 to biological relevant parameters
preorganisation of multi-dimensional data for statistical analysis
data formating for export
LemnaMiner Data analysis grids
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 96
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
LemnaBase
Handling large datasets
Software
Software: LemnaBase
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 98
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
LemnaShare
Connecting multiple users
Software
Software: LemnaShare
Date: 11/10/2010
Speaker: Matthias Eberius CMO Slide 100
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
LemnaCount
Quantifying biological objects
Software
Software: LemnaCount
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 102
Reliable count
counting high numbers
assessment of size, colour, shape
object classification
high reproducibility
LemnaTrack
Movement quantification software
Software
Software: LemnaTrack
Date: 11/10/2010
Speaker: Dr. Joerg Vandenhirtz CMO Slide 104
Quantifying movement
assessment of translational and within organism movement
life/death classification
spatial resolution of movement
movement patterns
visualising movement
References Most Global Players in Breeding and GMO are already using the LemnaTec Technology: BASF Pioneer Dupont Bayer CropScience Monsanto Syngenta Dow Agro Keygene IPK CSIRO ACPFG etc.
Visit our website www.lemnatec.com
Thank you for your attention!
Visit our website www.lemnatec.com
Time for your questions