Plant Sciences



  • ... take your plant research to the next level!  
  • ... take your plant research to the next level!
  • ... take your plant research to the next level!
  • ... take your plant research to the next level!

The Plant Sciences Facility (PlantS) operates 22 high quality state-of-the-art and highly specialized plant growth chambers and provides professional support to research groups at the VBC. Within spare capacities all services are also available for external customers. In 2017, PlantS initiated the Austrian Plant Phenotyping Network (APPN).

Several chambers are capable of providing exceptional environmental conditions i.e. low temperature (frost), high temperature, different light intensities, different light spectra and different gas conditions allowing precise environmental simulation across different climate zones and the simulation of various environmental stress conditions. Additionally, one of our chambers is equipped with a robotic plant phenotyping system.

If you are interested in our services and would like additional information or have specific project questions...
...get in touch with us!


    Digital Phenotyping & Image Analysis

    Digital Phenotyping & Image Analysis

    For objective, reproducible and high-throughput assessment of plant phenotypic traits, we operate an automated, chamber integrated, non-destructive screening system linked to LemnaTec image analysis software. Also external acquired images can be analyzed. Currently we are evaluating the software's capabilities towards custom phenotyping applications.

    If you are interested in our digital phenotyping & image analysis service and would like additional information or have specific project questions please feel free to contact Jakub Jez.

    High-Throughput Screening of Arabidopsis


    Several abiotic stress conditions can be applied (see environmental simulation service). Image acquisition can be conducted several times per day. Obtained plant leaf areas plotted over time will give you information about individual plant growth behavior (growth rates). Additionally, the morphological parameters listed on the right hand side can be acquired and plants can be grouped accordingly. 

    • chamber integrated system
    • highly controlled environment
    • sensor-to-plant system
    • visible light sensor
    • capacity: 1260 plants/pots
    • adjustable light spectrum (LED)
    • plant stress: cold (frost), drought & high light

     Image analysis i.a. :

    • Leaf area (→ growth rates)
    • Convex hull
    • Caliper length
    • Compactness
    • Roundness
    • Count and shape of leaves
    • Color classification

    Screening Of Arabidopsis Seedlings

    Input image

     Image analysis i.a. :

    • Count of seedlings
    • Leaf area (→ growth rates)
    • Convex hull
    • Caliper length
    • Compactness 
    • Roundness
    • Count and shape of individual leaves
    Results: image gallery (click to enlarge)
    Fig.2: leaf segmentation
    Projected Leaf Area of Col-0 and 4 different genotypes á 50 replicates exposed to different doses of UV-C (Mattia Dona, GMI)

    Custom Phenotyping: Side-View Plant Phenotyping

    treated                               control

    Custom phenotyping of Brachypodium distachyon
    Projected leaf area, 4 views/directions (Angelika Czedik-Eysenberg)

    Color classification

    Color classification

     Image analysis i.a. :

    • Leaf area (→ growth rates)
    • Height & Width
    • Convex hull
    • Compactness 
    • Color classification
    • Auto- or custom color classes (2-30)


    A.Djamei group, GMI

    Application note (LemnaTec): Color Classification.pdf

    Custom Phenotyping: Sunflower Seeds

    Image gallery: phenotyping sunflower seeds

     Image analysis i.a. :

    • Seed area/size
    • Height & Width
    • Roundness
    • Color classifications
    • Auto- or custom color classes (2-30)
    Image gallery: color classification


    Images kindly provided by Marco Todesco

    Application note (LemnaTec): Color Classification.pdf

    Root Development


    The skeleton algorithm can be perfectly applied on plant roots. Additionally, several morphological shoot parameters can be acquired and correlated with root results (Fig. 3). Over time image acquisition will give you information on individual root growth rates and lateral root development.


    W. Busch group, GMI



    Image gallery: Fig.1-3

    Currently available root parameters are:

    • Total root depth & width (Fig.1, yellow box)
    • Convex hull area and circumference (Fig.1, yellow hull)
    • length of the skeleton and of its individual bones (Fig.2, blue lines)
    • count of individual bones, count of end-bones (Fig.2, blue lines)
    • count of branching points/crossings (Fig.2, red dots)
    • Compactness
    • Shoot phenotyping (Fig.3)

    Image Analysis - Potential Applications

    We are currently evaluating LemnaTec's software capabilities. Potential applications include object recognition, count of objects, mobility tracking of objects (e.g. nematodes, larvae, labeled proteins), color classifications and the assessment of different morphological parameters like object size/area, circumference, convex hull, length, compactness, roundness etc.

    The skeleton algorithm can be applied on plant roots but as well on various other objects for example neurons or whole organisms. Potential results are the length of the skeleton and of its individual bones, the count of branching points and the orientation of individual bones.

    The image gallery illustrates several potential applications.

    We look forward to receiving your sample images with corresponding research questions to conduct first feasibility studies. 

    Image gallery: potential applications

    Environmental Simulation

    Environmental Simulation

    Several chambers are capable of providing exceptional environmental conditions like low temperature (≥ -15°C) high temperature (≤ +50°C) different light intensities & light spectra (LED-light: UV_375, blue_405, blue_450, white_warm & red_660_730) and different gas conditions (e.g. CO2 atmosphere). This allows precise environmental simulation across different climate zones and the simulation of various environmental stress conditions.

    If you are interested in our environmental simulation service and would like additional information or have specific project questions please feel free to contact Jakub Jez.

    Environmental simulation

    Fig.1 (click to enlarge)

    Fig.1 shows one example of successful environmental simulation: a Swedish August day.

    Temperature and humidity have been continuously recorded at the Swedish field site. Received data were imported as one-hour intervals with linear gradients between individual set points resulting in the successful simulation of a Swedish August day (temp. & hum.) in wintertime in Vienna, Austria.

    Fig.2: Spectral visualization of a sunset simulation (45min, linear light gradient)

    Abiotic Stress Response

    Various plant stress conditions can be conducted in highly controlled environments:

    • Cold stress (≥ -15°C)
    • Heat stress (≤ +50°C)
    • Light stress
    • Water stress (drought & partial watterlogging)

    Experiments concerning cold or water stress can also be performed in the Phenotyping Chamber.

    Pictures in the gallery (click to enlarge) show two examples of cold stress (Fig. 1 & 2) and one drought stress experiment (Fig. 3).



    Image gallery: Fig.1-3

    Basic Plant Growth

    Basic Plant Growth

    Our growth chambers provide standard plant growth conditions with only minor deviations from the set points, independent of external environmental influencing parameters. Significant deviations will be reported automatically 24/7. Temperature, humidity, light and water supply are computer controlled, fully automated and corresponding parameters are continuously graphed and documented.

    Additionally to the provided supplies, the facility also offers premises for soil preparation and plant handling, equipped with microscopes, a laminar flow hood etc. Two experienced technicians take care of the plants i.a. regarding aspects of pest monitoring and pest control.

    The image gallery will take you on a short tour through the PlantS Facility.

    Image gallery: Plant Sciences Facility

    Inter-Facility Services

    Inter-Facility Services

    Plant research related services of other VBCF Core Facilities and inter-facility cooperations.

    CRISPR Lab - Protein Technologies Facility

    CRISPR-Lab has established the CRISPR/Cas9 technology in A. thaliana, through a project funded jointly by CSF-ProTech and CSF-PlantS together with 10 labs from GMI, MFPL, BOKU and ISTA.

    The mission of CRISPR-Lab is to help VBC scientists in the optimal utilization of CRISPR/Cas9 technology by providing both knowledge and necessary customized materials.

    We provide the following A. thaliana services for gene knock-out projects:

    • Project design and generation of a binary vector containing Cas9 and guide RNAs
    • Above service plus transformation of A. thaliana with the desired construct (we provide unselected T1 seeds)
    • Above services plus selection (we provide T2 seeds from 10+ selected T1 plants)
    • Above services plus characterization of T2 plants (we provide T3 seeds with a verified frameshift mutation (indel))

    For knock-in projects and more details please visit the ProTech Facility homepage or contact Krzysztof Chylinski.

    Light Sheet Fluorescence Microscopy (LSFM) - Advanced Microscopy Facility

    Light sheet fluorescence microscope optimized for the 4D study of root growth. The geometry is such that light sheet is incident horizontally and imaging axis is from below (so as to capture cross-sectional slices of roots). A large sample chamber optimized for plant growth holds up to 5 seedlings, with fully programmable temperature control, external lighting conditions (day-night cycle), and drug/fluid-delivery to sample bath. Long working distance (8mm) high numerical aperture (NA 1.0) detection objective lens for high resolution imaging of large volumes. Digitally scanned light sheet with adjustable light sheet thickness, and 4 possible excitation laser lines (405nm, 491nm, 514nm and 561nm). Changeable magnification (25x, 37.5x, 50x), and imaging rates up to 100 frames per second on a large sCMOS camera chip. Custom user friendly software allowing for long time lapse imaging of selectable regions of interest. Also disposable to users is a powerful analysis workstation for performing e.g. deconvolution of images (various software) and stitching & visualization of images (Amira, Matlab, Fiji).

    For details please visit the AM Facility homepage or contact Kareem Elsayad

    Brillouin Scattering Microscopy (BSM) - Advanced Microscopy Facility

    A confocal-scanning microspectroscopy technique for the 3D all-optical label-free mapping of the viscoelasticity of live plant cells with sub-cellular resolution (~300nm laterally, ~600nm axially). Applications include phenotyping of cells and tissue based on the inherent mechanical properties. A parallel fluorescence confocal detection channel, and widefield transmitted light detection channel allow for correlative studies of chemical and morphological properties. Setup uses a 532nm excitation laser and custom analysis software for real-time spectral fitting and reconstruction of viscoelasticity maps.

    For details please visit the AM Facility homepage or contact Kareem Elsayad

    Protein Production

    In total more than 170m2 of high quality net plant growth space are available. We offer more than six years of experience in small- and large-scale purification of plant-derived proteins. Downstream processing focuses primarily, but not exclusively, on antibodies and antibody fragments and is accomplished through a close collaboration with the VBCF Protein Technologies Facility (ProTech)

    We have an open-minded approach to new collaborations and projects and look forward to your requests!

    Jakub Jez


    VBCF Plant Growth Chambers

    • 22 state-of-the-art plant growth chambers
    • 170m2 total net plant growth space
    • 90m2 Lab space
    • Computer assisted, precise control of environmental parameters
    • Temperature range from -15°C to +50°C
    • Humidity range from 30-80% rel. air humidity
    • Smart, gentle Air Circulation System
    • Adjustable light spectrum & intensity (LED-Chamber)
    • Fully automated Watering System
    • Robotic Plant Phenotyping System
    • Adjustable gas composition of atmosphere (CO2, etc.)
    • Air-Lock System equipped chamber for professional pathogen research
    • Large Capacity Chamber 
    • Documentation/graphing of environmental parameters
    Plant Sciences Facility Image Gallery

    Portable Fluorometer FluorPen FP 100-MAX-D (PSI)

    FluorPen is a portable, battery-powered fluorometer that enables quick and precise measurement of chlorophyll fluorescence parameters in the laboratory, greenhouse, or in the field. It can be effectively used for studying photosynthetic activity, stress detection, herbicide testing, or mutant screening:

    Record of two parameters:

    FT - continuous fluorescence yield in non-actinic light

    FTis equivalent to F0 if the leaf sample is dark-adapted.

    QY - Photosystem II quantum yield. 

    QY is equivalent to FV/FM in dark-adapted samples and to FV ' /FM ' in light-adapted samples. FV/FM is the most frequently used chlorophyll fluorescence parameter.

    Pre-defined protocols for measuring:

    OJIP Analysis 
    Application of chlorophyll fluorescence fast-transient analysis (OJIP) is a simple and non-invasive tool to monitor chloroplast function. Provided OJIP analysis is used as sensitive and reliable fast test for the functionality and vitality of photosynthetic system. 

    NPQ - Non-Photochemical Quenching 
    Provided are two predefined NPQ protocols differing in the duration of light exposure and dark recovery phase as well as in the number of intervals between the pulses. It is typically used for quantification of photochemical and non-photochemical quenching in dark-adapted samples.

    Light Curve 
    There are three predefined Light Curve protocols based on pulse modulated fluorometry differing in number and duration of single light phases and light intensities. Light Curve protocols provide successive measurements of the sample photosynthesis under various light intensities of continuous illumination relating the rate of photosynthesis to photon flux density.

    Sample holder: detachable leaf-clips

    suitable for experiments where long term dark adaptation is needed. They also allow simultaneous dark-adaptation of several leaves using several clips in situ under light, and then doing the readings one after another by attaching the device unit to each clip. 

    Cooperation with AGES

    In 2012, VBCF established a cooperation with AGES, the Austrian Agency for Health and Food Safety. Both institutions operate large-scale plant growth facilities with complementary technical specifications. The goal of the cooperation is the realization of research and development projects in life science by mutual use of technical scientific infrastructure, personnel, know-how, and operating resources.

    Austrian Plant Phenotyping Network (APPN)

    “Enhancing the Austrian Plant Phenotyping Community!”

    The APPN initiative aims to unite the Austrian plant phenotyping community in order to facilitate research collaborations, development of plant phenotyping infrastructure and methodologies, staff training, staff exchange and networking activities.

    For more informations please visit the APPN homepage:


    User Information



    In case of technical problems, pest infestations or other urgent issues please always write to:

    The pest management guideline can be found in MyVBCF for download.


    For detailed informations on our services and specific project requests please contact Jakub Jez.


    All new facility users have to attend a training in general plant rules. Please contact therefor Mrs. Anneliese Auer.

    The General Plant Rules can be found in MyVBCF for download.


    VBC member are encouraged to register to our BOOKING SYSTEM.

    External users should contact Jakub Jez.

    The booking system also provides you detailed information on the current environmental conditions, watering times, etc. 


    MyVBCF is the internal section of our homepage.

    You will find there documents, protocols and application notes for download and detailed information on light conditions (spectra, lux & µmol*s-1*m-2, light homogeneity, etc.)

    Information on the current temperature, humidity and on watering times of each individual chamber can be found in the Booking System.





    Citing the Facility

    The continuation of funding for VBCF by the City of Vienna and the Austrian Ministry of Science is dependent on documented evidence of contributions to scientific output. 

    Therefore it is absolutely required to acknowledge use of the facility when publishing work in which VBCF services were utilized.

    A simple statement is sufficient and can either be placed in the Materials and Methods section or in the Acknowledgements.

    Suggested format:

    The XXXXXX was performed by the Plant Sciences Facility at Vienna Biocenter Core Facilities GmbH (VBCF), member of Vienna Biocenter (VBC), Austria. 

    In case of (co-)authorship:

    The Vienna Biocenter Core Facilities GmbH (VBCF) Plant Sciences Facility acknowledges funding from the Austrian Federal Ministry of Science, Research & Economy and the City of Vienna.

    Your publication will then be listed on our website.


    The'PhenoBox', a flexible, automated, open-source plant phenotyping solution
    Czedik-Eysenberg, A., Seitner, S., Güldener, U., Koemeda, S., Jez, J., Colombini, M., & Djamei, A. (2018). The'PhenoBox', a flexible, automated, open-source plant phenotyping solution. The New phytologist. (abstract)


    Jakub Jez

    Jakub Jez

    Core Facility Head
    VBC2 / PG3

    Anneliese Auer

    Anneliese Auer

    Senior Technician
    VBC1 / 9.01

    Stefanie Koemeda

    Stefanie Koemeda

    Phenotyping Specialist
    VBC2 / PG3

    Klara Wuketich

    Klara Wuketich

    VBC2 / PG3

    Jolanta Ambroz Kumorowski

    Jolanta Ambroz Kumorowski

    VBC4 / 8.318



    Collaborations & Cooperations

    COST action FA1306

    The quest for tolerant varieties: Phenotyping at plant and cellular level.
    Management committee member


    In 2012, CSF established a cooperation with AGES, the Austrian Agency for Health and Food Safety. Both institutions operate large-scale plant growth facilities with complementary technical specifications. The goal of the cooperation is the realization of research and development projects in life science by mutual use of technical scientific infrastructure, personnel, know-how, and operating resources.



    Campus Vienna Biocenter

    Gregor Mendel Institute of Molecular Plant Biology

    Max F. Perutz Laboratories

    LemnaTec Gmbh

    University of Natural Resources and Life Sciences, Vienna

    Laura Bassi Centre PlantBioP - Plantproduced BioPharmaceuticals