Preclinical Imaging

  • Ultra high 15.2 T Bruker MR Imaging.
  • Ultra high 15.2 T Bruker MR Imaging.
  • Ultra high 15.2 T Bruker MR Imaging.

The Preclinical Imaging Facility (pcIMAG) provides comprehensive multimodal MR imaging. The main focus of the facility is in-vivo mouse imaging, while we welcome other smaller model organisms as well. Special emphasized is placed on state-of-the art data acquisition and processing.


    MR imaging data acquisition

    MR imaging data acquisition

    We offer a comprehensive list of services with focused application in neuroscience, cardiac imaging, anatomical characterization of organ systems and quantitative measurement of perfusion/MTT/Blood volume. Among the specific applications we offer cell labeling and tracking and axonal tract tracing using manganese (Mn2+) MRI.

    3D reconstruction of a mouse brain


    15.2T Bruker Biospec

    Bruker: FLASH sequence

    TR/TE: 160/3.5 ms

    Averages: 4

    Flip Angle: 15°

    Matrix: 200*160*80

    Resolution: isovoxel 0.1 mm

    3D reconstruction and Animation:

    6.0.0 Amira ©

    MR spectroscopy

    MR spectroscopy

    State of the art spectroscopy data acquisition brought to you by the highly optimized shim procedures developed by Bruker Biospin (Ettlingen, Germany). We are routinely performing spectroscopy of the brain, liver and in different tumor models.

    1H and 19F probes available.

    functional MRI

    functional MRI

    Functional magnetic resonance imaging is a technique for measuring brain activity. Regions with higher activation show an increase in the blood flow and the thus oxygen. fMRI is a tool to measure the changes in the oxygen concentration and gives you an activity map of the brain. It’s the perfect opportunity to study the influence of pharmacological, genetic and environmental manipulations on brain function.

    Quantitative image analysis

    Quantitative image analysis

    Sophisticated data processing and visualization is done using Amira, Drishti, ImageJ/FIJI and matlab. For more specific application in neuro-imaging we are using highly rated LONI pipeline (

    Mouse perfusion

    Mouse perfusion

    We offer mouse perfusion using Pressure Monitor BP-1 and ISMATEC pump, resulting in a Pressurized sacrificed perfusion. Both wash and fixing solutions are pressure controlled to ensure that they reach all the tissues.

    3D Printer

    3D Printer

    Together with the Advanced Microscopy Facility we purchased an Ultimaker 2 Extended 3D printer, allowing us to create specimen holder specifically desgined to our customers' requirements. We also offer 3D printing service to improve your own equipment.


    BioSpec 152/11

    Superconducting MagnetSystem

    • Field strength: 15.2 T
    • Diameter of clear bore: 110 mm
    • Stray-field (5 Gauss): +/- 2.3 m axial, +/- 2.5 m radial
    • Length: 1.591 m
    • Diameter: 1.362 m

    Gradient system B-GA 6S-100 with RT-shim and related power supplies

    • Actively shielded gradients
    • Integrated 2nd to 3rd shim set
    • Outer / inner diameter: 102 mm / 60 mm
    • Gradient amplitude: 750 mT/m
    • Slew rate: 9000 T/m/s
    • Water cooled

    RF coils

    1H Volume resonator T20054V3

    • Inner diameter 35mm
    • Maximum RF peak power 200 W @ 5ms
    • Continuous wave power 2W
    • Purpose : small animals body scans

    1H Volume resonator T20101V3

    • Inner diameter 23mm
    • Maximum RF peak power 200 W @ 5ms
    • Continuous wave power 1W
    • Purpose : small animals head scans

    1H/19F Volume resonator T20104V3

    • Inner diameter 35mm
    • Maximum RF peak power 200 W @ 5ms
    • Continuous wave power 2W
    • Purpose : small animals body scans on fluorine and proton frequency

    1H surface 4 segments array coil T20102V3

    • Inner diameter 32mm
    • Maximum RF peak power 250 W @ 5ms
    • Continuous wave power 2W
    • Purpose : small animals body scans

    Computer Hardware

    Z420 Hewlett-Packard Workstation equipped with :

    • Hardware: Intel(R) Xeon(R) CPU E5-1620 0 @ 3.6GHz, 4 Core(s), 32 GB Physical memory (RAM), 1 TB disk space
    • Software: operating system Linux Centos 5.9, ParaVision 6.0 software for control of MRI scanner, data acquisition and basic postprocessing

    2 x Z420 Hewlett-Packard Workstation equipped with :

    • Hardware: Intel(R) Xeon(R) CPU E5-1607 0 @ 3.00GHz, 4 Core(s),, 32 GB Physical memory (RAM), 2 TB disk space
    • Software: operating system Microsoft Windows 7 Professional, Amira - an extendable software system for scientific visualization, data analysis, and presentation of 3D and 4D data.

    Network-attached storage (NAS) server Thecus N10850

    • Intel® Xeon® E3-1225 3.1GHz Processor, 4 GB RAM, actual storage capacity 15 TB

    Featured Software : Paravision 6.0

    ParaVision® 6.0 is a new standard in preclinical MRI software that delivers unsurpassed image quality and enhanced productivity for both routine users and experts.


    • New and accelerated, intuitive workflow
    • Ready-to-use protocols and scan programs
    • Active method conflict handling
    • Automatic hardware recognition
    • Real-time optimization during scanning
    • On-the-fly RF-pulse calculation
    • In-line navigator-based image reconstruction
    • Fast 64 bit multi core image reconstruction for high resolution 3D imaging
    • Fully searchable data base, network data management
    • Remote scan planning and scheduling
    • Multi-modality scan planning
    • Arbitrary cuboid or ellipsoid shim volumes

    Technical features:

    • 3D Visualization and Analysis
    • Multimodal Data Import
    • Parallel Imaging and Reconstruction
    • Parallel Transmit
    • Project Planning
    • Method Development Framework

    On-site animal housing

    Preclinical Imaging facility is located on the ground floor of IMBA building (Vienna Biocenter), covering area of 82 sqm. Facility features 15.2 T Bruker Biospec and on-site animal housing facility with the capacity of 48 cages.

    User Information


    We welcome new projects. Investigators are invited to visit pcIMAG laboratory to learn more about our services. For more information or to schedule a visit to our facility please contact Jelena Zinnanti.

    Citing the facility

    How should I acknowledge The VBCF pcImaging Service?

    We all like to receive credit for the work we do don't we?
    Continuation of funding for the VBCF pcImaging facility by the city of Vienna and the ministry of science depends on documented evidence of contribution to scientific output.
    We therefore demand acknowledgement of utilization of the facility in publishing work.
    A simple statement is sufficient and can either be placed in the materials and methods section or at the end of your manuscript (acknowledgements) depending on journal format.

    Suggested format:
    The XXXXXX was performed by the Preclinical Imaging Facility at Vienna Biocenter Core Facilities (VBCF), member of Vienna Biocenter (VBC), Austria.

    In case of (co-)authorship:
    The Vienna Biocenter Core Facilities (VBCF) Preclinical Imaging Facility acknowledges funding from the Austrian Federal Ministry of Science, Research & Economy; and the City of Vienna.

    Pilot studies

    For your personal offer please contact Jelena Zinnanti.

    Cooperation Partners


    Brain-specific knockin of the pathogenic Tubb5 E401K allele causes defects in motor coordination and prepulse inhibition
    Martin W. Breuss, Andi H. Hansen, Lukas Landler, David A. Keays.
    Behav Brain Res. 2017 Apr 14;323:47-55.  (abstract)

    MAPK-activated protein kinase MK2 exerts immune regulatory functions in the microenvironment of orthotopic tumors
    Klara Soukup, Angela Halfmann, Fiona Poyer, Katharina Martin, Bernadette Blauensteiner, Bastien Huber, Mario Kuttke, Gernot Schabbauer, Lydia Zopf, Jelena Zinnanti and Alexander Michael Dohnal
    Cancer Res 2016;76(15 Suppl):Abstract nr A43; doi: 10.1158/1538-7445 (abstract)

    Mutations in the murine homologue of TUBB5 cause microcephaly by perturbing cell cycle progression and inducing p53-associated apoptosis.
    Martin Breuss, Tanja Fritz, Thomas Gstrein, Kelvin Chan, Lyubov Ushakova, Nuo Yu, Frederick W. Vonberg, Barbara Werner, Ulrich Elling, David A. Keays
    Development 2016 143: 1126-1133; doi: 10.1242/dev.131516 

    Quantification of plaque lipids in the aortic root of ApoE-deficient mice by 3D DIXON magnetic resonance imaging in an ex vivo model.
    Dietel B, Budinsky L, Kuehn C, Uder M, Achenbach S, Hess A.
    [Epub ahead of print] DOI 10.1007/s00330-014-3456-7 (abstract)

    Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function.
    Karaca E, Weitzer S, Pehlivan D, Shiraishi H, Gogakos T, Hanada T, Jhangiani SN, Wiszniewski W, Withers M, Campbell IM, Erdin S, Isikay S, Franco LM, Gonzaga-Jauregui C, Gambin T, Gelowani V, Hunter JV, Yesil G, Koparir E, Yilmaz S, Brown M, Briskin D, Hafner M, Morozov P, Farazi TA, Bernreuther C, Glatzel M, Trattnig S, Friske J, Kronnerwetter C, Bainbridge MN, Gezdirici A, Seven M, Muzny DM, Boerwinkle E, Ozen M; Baylor Hopkins Center for Mendelian Genomics, Clausen T, Tuschl T, Yuksel A, Hess A, Gibbs RA, Martinez J, Penninger JM, Lupski JR.
    Karaca, Ender et al. Cell , Volume 157 , Issue 3 , 636 - 650 (abstract)


    Jelena Zinnanti

    Jelena Zinnanti

    Core Facility Head
    VBC 2 / PG 3

    Jennifer Pizarro Pesado

    Jennifer Pizarro Pesado

    MRI Technologist
    Currently on leave

    Lydia Zopf

    Lydia Zopf

    MRI Technologist
    IMBA-GMI / 4.11

    Raphaela Hoefl

    Raphaela Hoefl

    IMBA-GMI / 4.11