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.
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.
Several phytotrons are capable of providing exceptional environmental conditions, allowing precise environmental simulation across different climate zones and various abiotic stress conditions.
- 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
The facility offers semi-automated phenotyping of various plant organs and growth stages, adapted to the needs of the customers:
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.
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.
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.
For detailed information on our services and specific project requests please contact Jakub Jez.
Training & general plant rules:
Need immediate assistance?
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.
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.
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. , 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. , PLoS Genet 16(7): e1008964.
Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin. Borg M et al. , 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 , Plant Cell doi.org/10.1105/tpc.20.00318
Versatile in vitro assay to recognize Cas9-induced mutations. Bente H, Mittelsten Scheid O, Donà M.  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  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.  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.  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.  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.  Elife 9:e58396.