PowerPoint Presentation LemnaTec

High throughput plant phenotyping for the development of better plants for the future

Matthias Eberius · CEO LemnaTec

Head of Research and Development

[email protected]

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


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


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


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


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


1. Scanning – infrared light

Quantify temperature differences (e. g. within leaves and between plants)

scanalyzer3D VIS imaging – shape


Scanning – visible light

High-resolution colour images for comprehensive morphological and growth phenotyping

2.

scanalyzer3D VIS imaging – colour


2. Scanning – visible light

Plant colour classification – Key to plant health, stress, nutrients and senecence

scanalyzer3D VIS imaging – architecture


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


Scanning – near infrared light for roots

spatial distribution of water content in soil

3.

0h 2h 4h 6h 8h

scanalyzer3D NIR imaging – shoot


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


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


movingfield

Automating plant handling

Plant transport 1-40 kg

randomisation

Precision watering

Multiple solution fertilising

Pesticide spraying

High density growth

Environment monitoring


movingfield – watering

individual plant watering

plant weighing

target humidity watering

multiple solution fertilising

top or bottom watering

salinity control

water logging

water use efficiency


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


high frequency imaging

changing neighbours

equilibrating hotspots (light, air humidity)



Impressions of the movingfield



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


high resolution imaging of trays and MTPs

scanalyzerHTS


high precision xy table

scanalyzerHTS special features


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


3D laser scanning

height of small plants

leaf angle

leaf movement

900 nm laser optional

scanalyzerHTS imaging


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


Analysing movement of small organisms

movement quantification

spatial distribution of movements

movement pattern

life/death classification

scanalyzerHTS feeding assays


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


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


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


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


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


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


Main program

DB / Grid / Miner

tree view

snapshot view

reanalyze

databaseadministration

run biotest



LemnaControlMonitoring the fully integrated automatisationof all LemnaTec scanalyzer systems

Software

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



LemnaGridImage analyzing software

Software

Software: LemnaGrid


Image analysis

Drag and drop modules

High flexibility

Transparent data flow

No programming languagenecessary

Self assembling imageanalysis wizard

Exclusive pluginalgorithms optional



Software: LemnaGrid – Wizard


Imaging GridWizard

parameterise eachanalysis step

direct visual feedbackon parameter changes

general explanationof algorithm function

context and grid specificcomments on algorithmfunction



LemnaMinerThe correlation software

Software

Software: LemnaMiner


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



LemnaMiner – Data analysis grids


Data analysis grids

drag and drop modules

high flexibility

Transparent data flow

no database languagenecessary

complex calculationswithin snapshots andtime series

biological datatransformation



LemnaBaseHandling large datasets

Software

Software: LemnaBase


Flexible data base

Linux PostgreSQLor Oracle

up to 100 TB

dynamic structure followingresult needs

maximum transparency

minimised access time

open interface for LIMS integration



LemnaShareConnecting multiple users

Software

Software: LemnaShare


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



LemnaCountQuantifying biological objects

Software

Software: LemnaCount


Reliable count

counting high numbers

assessment of size, colour, shape

object classification

high reproducibility

LemnaTrackMovement quantification software

Software

Software: LemnaTrack


Quantifying movement

assessment of translationaland within organismmovement

life/death classification

spatial resolution ofmovement

movement patterns

Visualising movement



Visit our website www.lemnatec.com

Thank you for your attention!

Visit our website www.lemnatec.com

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PowerPoint Presentation LemnaTec