Plant Sciences

IMPORTANT: Plant Sciences services at Covid-19 Re-Entry operation

For detailed information on the current facility operations, please click here.

Take your plant research to the next level!

 

ENVIRONMENT - PHENOTYPE - DATA

The Plant Sciences Facility (PlantS) operates 22 high quality and highly specialized plant growth chambers (phytotrons) and provides professional support to the outstanding “green research” at the Vienna BioCenter (VBC) and beyond.

The focus of the services provided is on environmental simulation, high-throughput (HT) plant phenotyping and subsequent image- and data analysis.

In 2017, PlantS initiated the Austrian Plant Phenotyping Network (APPN) with the goal to unite the Austrian plant phenotyping community and to support the ESFRI-EMPHASIS project.

SERVICES

High-throughput plant phenotyping

For the objective, reproducible and high-throughput assessment of plant phenotypic traits we operate numerous phenotyping devices for Arabidopsis and crop plants; shoot and root systems (see EQUIPMENT).

For the subsequent image analysis, we use classical image analysis approaches but also state-of-the-art deep learning pipelines. Data analysis, statistics and data visualization, up to publication-ready figures, complement the phenotyping service.

The phenotyping platform PHENOTron is designed for HT top-view RGB imaging of small plants like Arabidopsis thaliana and is fully integrated into one of our high-tech phytotrons:

 

The PHENOPlant infrastructure will strengthen and extend VBCF’s present HT plant phenotyping capabilities and the repertoire of sensors. The new platform is designed for mid-size crop plants as well as Arabidopsis and will be fully integrated into a state-of-the-art walk-in phytotron providing highly homogeneous plant growth conditions and allowing for dynamic environmental (live) simulations. Cutting-edge sensors will include multi-excitation PAM kinetic chlorophyll fluorescence, RGB, VNIR/SWIR hyperspectral, thermal and 3D.

We offer a complete HT phenotyping service: from seeds to data analysis, statistics and data visualization.

Environmental simulation

Several phytotrons are capable of providing exceptional environmental conditions, allowing precise environmental simulation across different climate zones and various abiotic stress conditions.

 

Simulated Environments:

  • Cold stress (≥ -15°C) & heat stress (≤ +50°C)
  • Water stress (drought & partial waterlogging)
  • Variable light intensity & spectrum (LED-light: blue_405nm, blue_450nm, warm_white & red_660_730nm) incl. spectral simulation of sunrise and sunset
  • CO2 level regulation

Custom Phenotyping and HT Image Analysis

The facility offers semi-automated phenotyping of various plant organs and growth stages, adapted to the needs of the customers:

  • PHENOBox: Side-view phenotyping of tall plants and agar-plates (seedlings).

  • PHENOScan: Agar-plate based screening of Arabidopsis roots.

  • HT Image Analysis: High-throughput image analysis service.

EQUIPMENT

Walk-in phytotrons

With 22 high-quality, state-of-the-art and highly specialized plant growth chambers, PlantS can precisely control environmental conditions, reproducing abiotic plant stress conditions such as frost, drought and various spectral light and CO2 gas conditions. Furthermore, we can accurately simulate various global environmental conditions from a range of different climate zones.

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The phenotyping platform PHENOTron

The phenotyping platform (PHENOTron) is designed for top-view RGB imaging of small plants like Arabidopsis thaliana and is fully integrated into one of our high-tech phytotrons.

This particular phytotron facilitates frost stress experiments (> -15°C) and is equipped with a high-tech LED light with adjustable light spectrum.

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Visualisation of PHENOPlant

Multi-Sensor, High-Throughput Plant Phenotyping Platform. Coming in 2021.

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Angelika Czedik-Eysenberg et al., New Phytologist 2018

A system for phenotyping of individual tall plants, e.g. model grass Brachypodium distachyon or maize. Coupled with PhenoPipe module for calculation of multi-dimensional distances from phenotyping data, we provide an affordable, automated, open source imaging and data processing solution that can be adapted to various phenotyping applications in plant biology and beyond.

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PHENOScan

Agar-plate based screening of Arabidopis roots

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USER INFORMATION

In case of any questions on our services/equipment and for project requests please contact the Facility Head Jakub Jez.

Project requests:

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

 

Training & general plant rules:

All new facility users must attend a training session on general plant rules. Please contact Mrs. Anneliese Auer. The General Plant Rules can be found in MyVBCF for download.

 

Need immediate assistance?

In case of technical problems, pest infestations, or other urgent issues please always write to: plants(at)vbcf.ac.at. The pest management guidelines can be found in MyVBCF for download.

 

Booking system

The continuation of funding for VBCF by the City of Vienna and Austrian Federal Ministry of Education, Science and Research is dependent on documented evidence of contributions to scientific output. Therefore, it is mandatory to acknowledge use of the facility when publishing work for which VBCF services were used.

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 the 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 Education, Science and Research and the City of Vienna. (Your publication will then be listed on our website.)

PUBLICATIONS

Autophagy mediates temporary reprogramming and dedifferentiation in plant somatic cells
Rodriguez E, Chevalier J, Olsen  J, Ansbøl  J, Kapousidou  V, Zuo  Z, Svenning  S, Loefke  C, Koemeda  S, Serrano Drozdowskyj  P, Jez  J, Durnberger  G, Kuenzl  F, Schutzbier  M, Mechtler  K, Nagel Ebstrup  E, Lolle  S, Dagdas  Y, Petersen M. EMBO J (2020).

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. The New Phytologist, 2018.