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!



The Plant Sciences Facility (PlantS) operates 23 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.


High-throughput plant phenotyping

For objective, reproducible and high-throughput assessment of plant phenotypic traits we operate numerous phenotyping instruments 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. We offer a complete HT phenotyping service: from seeds to data analysis, statistics and data visualization.

Multi-sensor, high-throughput plant phenotyping platform - PHENOPlant


PHENOPlant is designed for non-invasive, morphometric and physiological hight-throughput plant phenotyping of 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.

Furthermore, the platform facilitates precise environmental (live) simulations across different climate zones as well as controlled plant stress experiments. Cutting-edge sensors include multi-excitation PAM kinetic chlorophyll fluorescence, RGB, VNIR/SWIR hyperspectral, thermal and 3D.

Within the planned infrastructure, plants are transported on conveyor belts from the growth area to the imaging cabinets equipped with state-of-the-art sensors. The imaging units are physically seperated from the growth area (two individually controlled phytotrons) facilitating the parallelization of measurements via a sample loop and thus improving the throughput, flexibility and sensor utilization. 

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:

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.


Walk-in phytotrons

With 23 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.

Read more

PHENOPlant is designed for non-invasive, morphometric and physiological hight-throughput plant phenotyping of 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.

Read more

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.

Read more

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.

Read more


Agar-plate based screening of Arabidopis roots

Read more


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) The pest management guidelines can be found in MyVBCF for download.


Booking system

We require acknowledgement of facility use in publications. 
A simple statement is sufficient and can be placed in the Materials and Methods section or in the Acknowledgments section, depending on the journal format.

Suggested format:

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

In case of (co-)authorship:

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


Application of expansion microscopy on developing Arabidopsis seeds. Kao P, Nodine MD. Methods Cell Biol. 2021;161:181-195.

Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis. Borg M, Papareddy RK, Dombey R, Axelsson E, Nodine MD, Twell D, Berger F. Elife. 2021 10:e61894.

Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure. Bente H, Foerster AM, Lettner N, Mittelsten Scheid O. PLoS Genet. 2021 17(3):e1009444.

The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W. Osakabe A, Jamge B, Axelsson E, Montgomery SA, Akimcheva S, Kuehn AL, Pisupati R, Lorković ZJ, Yelagandula R, Kakutani T, Berger F.  Nat Cell Biol. 2021 23(4):391-400.

Signatures of antagonistic pleiotropy in a bacterial flagellin epitope. Parys K, Colaianni NR, Lee HS, Hohmann U, Edelbacher N, Trgovcevic A, Blahovska Z, Lee D, Mechtler A, Muhari-Portik Z, Madalinski M, Schandry N, Rodríguez-Arévalo I, Becker C, Sonnleitner E, Korte A, Bläsi U, Geldner N, Hothorn M, Jones CD, Dangl JL, Belkhadir Y. Cell Host Microbe. 2021 29(4):620-634.e9.

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).

Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin. Montgomery SA et al. [2020], Current Biology 30:4, 573-588.e7

The evolution and functional divergence of the histone H2B family in plants. Jiang D, Borg M, Lorković ZJ, Montgomery SA, Osakabe A, Yelagandula R, Axelsson E, Berger F. [2020], PLoS Genet 16(7): e1008964. 

Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin. Borg M et al. [2020], Nature Cell Biology 22: 621–629

ARADEEPOPSIS, an Automated Workflow for Top-View Plant Phenomics using Semantic Segmentation of Leaf States. Hüther P, Schandry N, Jandrasits K, Bezrukov I, Becker C [2020], Plant Cell 

Versatile in vitro assay to recognize Cas9-induced mutations. Bente H, Mittelsten Scheid O, Donà M. [2020] Plant Direct. 4: 1– 13.

Chromatin regulates expression of small RNAs to help maintain transposon methylome homeostasis in Arabidopsis. Papareddy RK, Páldi K, Paulraj S, Kao P, Lutzmayer S, Nodine MD [2020] Genome Biology 21, 251.

Arabidopsis shoot stem cells display dynamic transcription and DNA methylation patterns. Gutzat R, Rembart K, Nussbaumer T, Hofmann F, Pisupati R, Bradamante G, Daubel N, Gaidora A, Lettner N, Donà M, Nordborg M, Nodine M, Mittelsten Scheid O. [2020] EMBO J. 39(20):e103667.

A high-throughput screening method to identify proteins involved in unfolded protein response of the endoplasmic reticulum in plants. Alcântara A, Seitner D, Navarrete F, Djamei A. [2020] Plant Methods. 16:4.

Ribosome assembly factor Adenylate Kinase 6 maintains cell proliferation and cell size homeostasis during root growth.Slovak R, Setzer C, Roiuk M, Bertels J, Göschl C, Jandrasits K, Beemster GTS, Busch W. [2020] New Phytol. 225(5):2064-2076.

A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress.Stephani M, Picchianti L, Gajic A, Beveridge R, Skarwan E, Sanchez de Medina Hernandez V, Mohseni A, Clavel M, Zeng Y, Naumann C, Matuszkiewicz M, Turco E, Loefke C, Li B, Dürnberger G, Schutzbier M, Chen HT, Abdrakhmanov A, Savova A, Chia KS, Djamei A, Schaffner I, Abel S, Jiang L, Mechtler K, Ikeda F, Martens S, Clausen T, Dagdas Y. [2020] Elife 9:e58396.

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.