Advanced Microscopy

The Advanced Microscopy Facility provides access, training and technical assistance for researchers to an expanding inventory of cutting edge and novel optical imaging techniques. We also have an R&D lab that develops novel and custom tailored optical microscopy solutions for specific life science and biomedical research needs.

What's new? 

  • December 2017 : Stayin' Alive - Interreg V-A - Austria-Czech Republic workshop on live-cell imaging techniques available at AM, 12. January 2018. Because of large demand, we offer 2 extra lattice light sheet demo session on 23.01.2018.
  • November 2017 : Interested in doing an internship at our facility? Feeling at home in software engineering? Experience in Matlab / .NET or any other system level programming is welcome. We have some projects in data analysis & instrument control. Longer internship 4M+ preferred. Feel free to contact us at
  • May 2017 :  Welcome our new microscope LaVision Ultramicroscope. Another great addition to our light-sheet family. This one is especially great for large samples up to 1 cm.
  • January 2018: The COST funded BioBrillouin- / EMBL- Training school “Brillouin Microscopy: Emerging Tool for Probing Mechanical Properties of Living Cells” (which we co-organized) was successfully held at EMBL on 17-19th January (for more info see
  • July 2017: We congratulate Dr. Dea Slade on being awarded a WWTF NEXT grant (for which we are co-applicants). The grant funds the further improvements of the add on module that has been developed in the facility for UV DNA damage/repair studies in close collaboration with the Slade lab.


    Available techniques

    Available techniques

    We offer several techniques for routine use, consisting of commercial and self-built instruments. These include:

    Light sheet & super-resolution microscopy:

    • Lattice Light Sheet (LLS)                                       - For live cell studies with minimal phototoxicity
    • Selective Plane Illumination Microscope (SPIM)  - Ideal for long term root growth studies
    • UltraMicroscope II                                                  - Light sheet optimized for cleared macroscopic samples
    • 3D Structured Illumination Microscopy (SIM)      - For fast super-resolution colocalization experiments 
    • Total Internal Reflection Microscopy (TIRF)        


    • Fluorescence Lifetime Imaging Microscopy [Time-Domain] (FLIM)
    • Fluorescence Correlation and cross-correlation Spectroscopy (FCS & FCCS)
    • Fluorescence Lifetime Correlation and Cross-Correlation Spectroscopy (FLCS & FLCCS)
    • Steady-state & Time-Resolved Fluorescence Anisotropy (TRFA) Imaging
    • Brillouin Light Scattering Microscopy (BLSM), with fluorescence measurements (FBi)

    In addition we can offer :

    • Assistance with image analysis 
    • Need custom tailored microscopy imaging system ? Please check our Microscope development section.
    • Fast dual camera widefield fluorescence imaging (405, 488, 561 & 640 nm excitation lines)
    • Differencial Interference Contrast (DIC) imaging
    • Objective- or Stage- scanned confocal microscopy (fluorescence or scattering)

    If you are interested in using any of the above techniques please see below under "Start up / Pilot Studies" or just send us an email at


    Trained users only :  Book a microscope

    Microscope development

    Microscope development

    The Advanced Microscopy Facility develops custom and novel optical microscopy solutions for biomedical research applications at the Vienna Campus Biocenter.

    They are developed by a dedicated team of physicists & biologists , who also assist end users in operating the instruments. After an optimization phase the developed microscopes become part of our “Available Techniques” and can be used by all interested researchers.


    The microscopes we develop are based on demand and potential-demand of the researchers on the Vienna Campus Biocenter.

    Our policy – the Instrument Credit Point (ICP) policy – involves securing partial external/user funding for the development of microscopes prior to development. Once a critical mass of external/user funding is guaranteed, we begin development. A strong incentive for users contributing to the pre-financing of instruments is that they in turn receive free usage of the instrument for a fraction of available user hours corresponding to their contribution to the total cost of the instrument. An additional incentive is that the instrument and any developed software will be optimized for their applications already in the construction phase, and will thus be better suited for their desired applications.

    We are always on the lookout for new microscope projects, and would love to hear your suggestions. If we can gather enough potential interest we may go ahead and build it for you!

    Our projects may roughly be divided between “safe” and “cutting-edge”. The former are generally clones of instruments that have already been realized with minor modifications, the applications and type of results one can obtain from these are well defined. The latter have the potential for more novel or specialized applications, and will generally involve introducing or adapting a more exotic imaging modality to biomedical research applications. Depending on demand and financing we try to do a bit of both.

    If you would like to get up to date information on planned / proposed projects you can sign up to our mailing list by sending us a quick note to


    We also perform so-called Mini-projects, which involve building modifications to existing microscopes or small custom setups that users can use/keep in their labs. The time scales (and corresponding workloads) for these are also generally shorter. For more information about this service please contact us.

    Workshops & Events

    Workshops & Events

    Running Seminar Series & upcoming workshops hosted by us :



    Recent talks/presentations :

    • 25-26 Sep 2014 - Poster presentation at 1st Light-Sheet Fluroescence Microscopy Conference (Barcelona, Spain)
      "Long Term Live Imaging of Primary Root Growth in Arabidopsis sp. with LSFM"
      (E. Sanchez, L. Zhang, et. al. )
    • 19 Sep. 2014 @ 10:00 (ISTA, Austria)
      "Mapping Viscoelasticity with Brillouin Scattering Microscopy: Biological Applications (K. Elsayad)
    • 15 Sep. 2014 @ 10:50 (Biophysical Meeting / 6th OEGMBT Annual Meeting, Austria)
      "Microscopes at the CSF Advanced Microscopy Facility" (K. Elsayad)
    • 25 Aug. 2014 @ 14:00 (IMP Seminar Room #2)
      "Betzig SPIM Info Session" (CSF Advanced Microscopy Team)
    • 13 Feb. 2014 @ 14:00 (IMBA Main Lecture Hall)
      "The Stessoscope"
      (K. Elsayad) (Introduction to a newly available microscope)
    • 28 Oct. 2013, @14:00 (MUE- Anna Spiegel Forschungsgebaeude)
      "CSF Advanced Microscopy: Instruments, Projects & Policies" (K. Elsayad)
    • 12 Nov. 2013 @ 10:00 (as part of 2nd Max F. Perutz Lab FLIM & FCS Workshop)
      "Getting and making the most out of Fluorescence Lifetimes" (K. Elsayad)
    • 13 Nov. 2013 @ 11:00 (as part of 2nd Max F. Perutz Lab FLIM & FCS Workshop)
      "Microscopes at the CSF: Current & Planned" (E. Sanchez)

    Other microscopy/optics related conferences & events :

    Micro Wiki

    Micro Wiki

    Visit our wiki, and learn more about the technology/theory behind our available techniques, their current status, as well as other interesting microscopy trivia.



    Lattice Light Sheet Microscope

    Lattice light sheet

    Lattice light sheet developed by Nobel Laureate Prof. Eric Betzig allows capture at sub-second resolution full three-dimensional dynamics, at diffraction limit or beyond. The promise of the lattice light sheet is to provide minimal photobleaching and phototoxicity unmatched to any other fluorescence microscopy technique available.


    ·         Tracking of mitotic microtubule

    ·         Embryogenesis

    More details here.

    ·         Diffusion of molecules in cell spheroids

    Light sheet fluorescence microscopy

    L-SPIM is a custom built selective plane illumination microscope (light sheet microscope), optimized for high-throughput plant studies, but also useful for volume imaging of other large, cleared/optically transparent samples in mm range.

    The setup currently allows for imaging volumes up to 8mm into a sample for a single volume run, with the added benefits of reduced phototoxicity - orders of magnitude better than scanning confocal microscopy - and excellent contrast in the axial dimension even deep within samples.

    Because SPIM is a widefield imaging technique (only the optical imaging axis direction is physically scanned) it is also very fast, and one can obtain high frame rate volume images with ease. The imaging rate is in practice usually dependent on the camera exposure time per frame  - which in turn is ultimately dependent on the labeling and the sample - and the desired field of view/resolution.

    For most applications, acquisition of 500 slice z-stack, is possible in less than a minute.

    The L-SPIM offers a unique imaging/excitation geometry motivated by the initially intended application of studying plant root growth, where the light sheet is incident horizontally and imaging is from an objective below the sample (the name L-SPIM is derived from the initially "L-shaped" sample holder).


    Root development specific modifications :

    Numerous modifications for plant studies have been added, including a microfluidic system allowing for the content of the imaging chamber in which the sample is in to be exchanged during imaging runs (to test e.g. the effects of different drugs), as well as a computer controlled ‘daylight lamp’ that is programmed to mimic day/night cycles.

    Multiposition high-throughput root tracking and position focus correction are under active development.


    The versatility of the setup has resulted in the instrument having also found a range of applications beyond plant root studies including the imaging of various organisms (e.g. mammalian tissue, drosophila embryos, zebrafish, c. elegans).

    For more information on the setup see here.

    Time-resolved Confocal Fluorescence Microscope with Excelent Single Molecule Sensitivity

    Fluorescence Lifetime Imaging Microscope (FLIM) measures the so-called total fluorescence lifetime of fluorophores - as in, how long on average a fluorophore stays in it's excited state following excitation from a short excitation light pulse. This can give you a wealth of information on the fluorophores local (at nanometer scale) chemical and physical environment.

    It can also be used to study translational and rotational behaviour of the fluorophores and their relative orientations and orientational dynamics (and thereby often also allow you to estimate those of whatever said fluorophores are bound to).


    Further technical details about our setup can be found here

    3D Structured Illumination Microscope

    3D Structed Illumination Microscope

    3D Structured Illumination Microscope (3D SIM) is a fluroescence microscopy technique capable of achieving down to 100-200 nanometers lateral (xy) resolution and a very good (meaning better than normal) axial (z) resolution*. The 'trick' used for achieving the increased spatial resolution is to modify the 3d spatial excitation field profile such that only select patterned regions of the sample are excited for each image acquisition cycle. Computational analysis of a set of consecutive images with distinct spatial illumination profiles are then used to calculate a 3d image with a better spatial resolution than can be achieved by conventional optical far-field imaging*. Due to the fast sensitive cameras the microscope setup is also well suited for very fast conventional (widefield) fluorescence imaging. Further technical details about our setup can be found here

    Brillouin Scattering Microscope

    Our Brillouin Scattering Microscope (BSM) is a confocal-scanning implementation of a spectroscopy technique -Brillouin Scattering spectroscopy, which allows for all-optical label-free spatial mapping of the viscoelastic properties of materials. 

    To measure the Brillouin Spectrum one probes the sample with a single-frequency laser and measures the GHz-scale (<0.0001nm wavelength) spectral modification scattererd light. This spectrally-shifted light - typically measured in the back-scattering configuration, is the result of light scattering from inherent collective thermal density fluctuations with the sample, and can be used to calculate the hypersonic velocity in the probed region. Given knowledge of the density and effective refractive index of the probed region one can then calculate the viscoelasticity of the sample, specifically the bulk longitudinal storage and loss moduli – in the GHz regime.

    Our setup allows for the combination with fluorescence or Raman scattering detection such that one can correlate the viscoelasticity and fluorescence or Raman spectra on a pixel-per-pixel level. The required acquisition times in order to get reasonable estimates of the viscoelasticity are on the order of several seconds per pixel for typical samples. We can achieve a spatial resolution down to ~300nm laterally, and can produce 3d viscoelasticity for reasonably transparent samples.

    The technique is starting to find increasing applications in medical diagnostics and biomedical research.

    For more information see here.

    Resources available at Partner Institutions

    User Information

    Start up / pilot studies

    Pilot Studies

    We offer “Pilot Studies” on all our instruments where for 70 EUR/hr we will test your samples on the required microscope. All imaging in this case will be performed by an Advanced Microscopy Facility staff member who will also discuss the outcome of the study. 

    General Usage

    Due to limited personnel time pilot studies at this price cannot be scheduled for more than 2 hrs. Following the 2 hr limit personnel and instrument time will thus be charged at the standard rate. For information on rates please contact us at 

    Following a successful pilot study the user is also recommended to schedule a full training on the instrument, which will give them a better understanding of the technique/instrument and allow them to use the instrument unsupervised. After satisfactory completion of the training the user is granted access to our online booking system where they can reserve the instrument as desired. To respect all users we have implemented a 24 cancellation policy, following which the standard hourly charge is incurred.


    If you have used one of our instruments to obtain results presented in a manuscript or other publication we request that you acknowledge us as follows

    “We acknowledge the Advanced Microscopy Facility (advMICRO) of the Vienna Biocenter Core Facilities (VBCF), member of the Vienna Biocenter (VBC) Austria, for [service + description of microscope]“

    If members of the facility have contributed scientifically to the results or the process of obtaining the results in your manuscript, and you would like to acknowledge them as coauthors, please contact us to assure that funding sources relevant to the project are correctly acknowledged.

    Collaborations / Visits

    Research / collaboration

    • Miloš Šramek, Gregor Mendel Institute, Development of root tracking strategies 
    • Hamid [homepage]
    • Benjamin Schreiber, Biophotonics Group, Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 2016

    FemTech Alumni : 

    • Paula Hyks, Development of control algorithms for temperature stabilization, L-SPIM
    • Angela Koffler, Development of PID compensation of laser fluctuations at sample, L-SPIM
    • Franziska Gartner, Measurement of Raman spectra of selected histopathology samples



    Feedback / Question


    p62 filaments capture and present ubiquitinated cargos for autophagy.
    Gabriele Zaffagnini, Adriana Savova, Alberto Danieli, Julia Romanov, Shirley Tremel, Michael Ebner, Thomas Peterbauer, Martin Sztacho, Riccardo Trapannone, Abul K Tarafder, Carsten Sachse, Sascha Martens.
    The EMBO journal, e98308. (abstract)

    β-Catenin–dependent mechanotransduction dates back to the common ancestor of Cnidaria and Bilateria.
    Ekaterina Pukhlyakova, Andrew J. Aman, Kareem Elsayad, and Ulrich Technau.
    Proceedings of the National Academy of Sciences115(24), 6231-6236. (abstract)

    Host-Polarized Cell Growth in Animal Symbionts.
    Pende, Nika, Jinglan Wang, Philipp M. Weber, Jolanda Verheul, Erkin Kuru, K-MR Rittmann Simon, Nikolaus Leisch et al.
    Current Biology, 28(7), 1039-1051. (abstract)

    Axicon-based Bessel beams for flat-field illumination in total internal reflection fluorescence microscopy

    Benjamin Schreiber, Kareem Elsayad, and Katrin G. Heinze

    Optics Letters 42(19):3880-3883 (2017)

    A novel non-canonical PIP-box mediates PARG interaction with PCNA

    Tanja Kaufmann, Irina Grishkovskaya, Anton A. Polyansky, Sebastian Kostrhon, Eva Kukolj, Karin M. Olek, Sebastien Herbert, Etienne Beltzung, Karl Mechtler, Thomas Peterbauer, Josef Gotzmann, Lijuan Zhang, Markus Hartl, Bojan Zagrovic, Kareem Elsayad, Kristina Djinovic-Carugo, Dea Slade

    July 2017 Nucleic Acids Res gkx604

    Abstract & full text

    Fluorescence Excitation, Decay, and Energy Transfer in the Vicinity of Thin Dielectric/Metal/Dielectric Layers near Their Surface Plasmon Polariton Cutoff Frequency

    K. Elsayad and K. Heinze. Chapter 6, Page 111 in "Surface Plasmon Enhanced, Coupled and Controlled Fluorescence" (1st Edition, Edited by C. Geddes)

    (C) 2017 John Wiley & Sons, Inc. [ISBN: 978-1-118-02793-6]

    PI (3, 4, 5) P 3 Engagement Restricts Akt Activity to Cellular Membranes  

    Michael Ebner, Iva Lučić, Thomas A. Leonard, Ivan Yudushkin
    Molecular Cell 65(3):416-431 (2017). DOI: 10.1016/j.molcel.2016.12.028

    Localization of mTORC2 activity inside cells  

    Michael Ebner, Benjamin Sinkovics, Magdalena Szczygie, Daniela Wolfschoon Ribeiro, Ivan Yudushkin
    J Cell Biol Jan 216(2):343-353 (2017). DOI: 10.1083/jcb.201610060



    Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission–Brillouin imaging
    Kareem Elsayad, Stephanie Werner, Marçal Gallemí, Jixiang Kong, Edmundo R. Sánchez Guajardo, Lijuan Zhang, Yvon Jaillais, Thomas Greb and Youssef Belkhadir
    Sci. Signal. 05 Jul 2016: Vol. 9, Issue 435, pp. rs5

    (Abstract & Full Text)

    The expression of tubb2b undergoes a developmental transition in murine cortical neurons
    Martin Breuss, Jasmin Morandell, Simon Nimpf, Thomas Gstrein, Mattias Lauwers, Tobias Hochstoeger, Andreas Braun, Kelvin Chan, Edmundo R. Sánchez Guajardo, Lijuan Zhang, Marek Suplata, Katrin G. Heinze, Kareem Elsayad and David A. Keays.
    Journal of Comparative Neurology
    Volume 523, Issue 15, pages 2161–2186, 15 October 2015

    Membrane Protein Localization by SpecON.
    K.G.Heinze, K. Elsayad.
    Imaging & Microscopy16:23

    Mal3, the Schizosaccharomyces pombe homolog of EB1, is required for karyogamy and for promoting oscillatory nuclear movement during meiosis.
    Polakova S., Benko Z., Zhang L., Gregan J.
    Cell Cycle. 13:72 (abstract)

    Spectrally coded optical nanosectioning (SpecON) with biocompatible metal–dielectric-coated substrates.
    K. Elsayad, A. Urich, P.S. Tan, M. Nemethova, J.V. Small, K. Unterrainer, K.G.Heinze.
    Proc.  Nat. Acad. Sci USA 110:20069 (abstract)


    Kareem Elsayad

    Kareem Elsayad

    Core Facility Head
    MFPL 00 / 1.108

    Juraj Gregan

    Juraj Gregan

    Visiting Scientist
    VBC6 / K290

    Elisabeth Holub

    Elisabeth Holub

    Hamid Keshmiri

    Hamid Keshmiri

    Research Technician
    VBC6 / K290

    Edmundo Ricardo Sanchez Guajardo

    Edmundo Ricardo Sanchez Guajardo

    R&D Scientist
    MFPL 00 / 1.108

    Marek Suplata

    Marek Suplata

    R&D Scientist
    MFPL 00 / 1.108

    Lijuan Zhang

    Lijuan Zhang

    R&D Scientist
    MFPL 00 / 1.108

    Natascha Weinberger

    Natascha Weinberger

    Research Technician
    MFPL 00 / 1.108


    Advanced Microscopy Applications Specialist (m/f)

    The VBCF Advanced Microscopy Facility is currently seeking a highly motivated, full-time Advanced Microscopy Applications Specialist (m/f).

    The Vienna Biocenter Core Facilities (VBCF) offers cutting-edge technologies for life science researchers at the Vienna Biocenter Campus and beyond. The Advanced Microscopy facility provides researchers with a diverse selection of advanced optical microscopy and spectroscopy techniques, which include light sheet microscopy, superresolution microscopy, as well as time-resolved (fluorescence correlation, fluorescence lifetime) and wavelength resolved microscopy/spectroscopy setups. The facility is equipped with state-of-the-art commercial and self-built microscopes as well as imaging software (

    The responsibility of the Advanced Microscopy Applications Specialist will be to assist users on selected instruments in the form of training, operation, experimental guidance / project planning, sample preparation as well as data evaluation. The person filling this position will also be responsible for instrument maintenance as well as regular performance checks and calibration/alignment as needed.

    Applicants should ideally hold a PhD in a relevant field and should have a minimum of 3 years of experience directly related to the job description. A solid background in light-microscopy techniques and their application to biological questions as well as the readiness to teach and work with multiple users is a must. Experience in instrument control and image analysis using Labview and Matlab is a strong asset.

    The candidate should be able to work as part of a team, be highly self-motivated, reliable and well organized. Fluency in English together with good communication and interpersonal skills are required. The candidate should be an enthusiastic, service-oriented team player willing to assist diverse life science researchers with basic and advanced aspects of optical microscopy and spectroscopy.

    The VBCF, embedded in the Vienna BioCenter (VBC), is offering the opportunity to work in a dynamic international environment with excellent benefits including a child support center, subsidized cafeteria and training courses. The yearly gross salary will be commensurate to qualification and experience. The position is available from beginning of 2019 and is initially limited to 1 year with the possibility to prolong subject to satisfactory performance.

    Applications, including a full CV, motivation letter, and contact information of three or more references should be sent electronically to:

    1. I want you to know...

    2. Good experience, bad experience, suggestion for improvements, etc.. Please leave your anonymous (or non-anonymous) feedback on your experiences working with Advanced Microscopy Facility here...
    1. I have a Microscopy Question...

    2. Have a question related to one of our microscopy techniques or instruments? Go ahead and ask us - we're happy to help!

    Lattice Light Sheet Microscope

    Microscope Description


    Lattice light sheet developed by Nobel Laureate Prof. Eric Betzig allows capture at sub-second resolution full three-dimensional dynamics, at diffraction limit or beyond. The promise of the lattice light sheet is to provide minimal photobleaching and phototoxicity unmatched to any other fluorescence microscopy technique available.


    Lateral resolution

    Dithered mode                                              

    Structural illumination mode                


    AXIAL resolution

    Dithered mode                                              

    Structural illumination mode             

    Field of view



    405 nm

    488 nm

    561 nm

    642 nm



    Fundamental limits

    • Optimal Penetration depth is in the range of 20 – 30 um. With lowered resolution the upper limit is  around 100 um.
    • Imaging medium must be as much transparent with low turbidity as possible.


    ·         Tracking of mitotic microtubule

    ·         Embryogenesis

    ·         Diffusion of molecules in cell spheroids




    Useful LInks


    Bi-Chang Chen et al, Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution, Science  24 Oct 2014, Vol. 346, Issue 6208, 1257998
    DOI: 10.1126/science.1257998


    We gratefully acknowledge the Wiener Wissenschafts- Forschung- und Technologiefonds for supporting this project, WWTF grant # LS14-009.


    Delta Vision OMX (3d SIM)

    by Applied Precision (GE Healthcare)

    • lateral (xy) resolution for 3d SIM: δx,δy≈110 nm at λ=405nm (deep-blue); δx,δy≈170 nm at λ=593nm (yellow);
    • axial (z) `resolution' for 3d SIM:  δz≈300 nm 4 excitation Laser wavelengths available: 405nm, 488nm, 568nm & 640nm.
    • No `special' fluorophores required (anything that can be excited by the above lasers and emits within the range of the emission filters).
    • Temperature control available for live cell imaging
    • Laser controlled autofocus
    • 2 sCMOS cameras allowing simultaneous imaging in two colours. Suitable also for very fast dual-colour conventional (non- 3d SIM) imaging. Imaging rates doubled for tri-colour imaging.

    FLIM Microscope setup

    Olympus iX71 inverted microscope frame

    (manufacturer website)

    Widefield / condensor illumination: Xcite-120 Metal-halide source.

    "MicroTime 200" setup


    • Computer controlled Multichannel Picosecond Diode Laser Driver "Sepia II"
    • LDH-D-C-510  [laser head (pulsed & CW), wavelength = 510(+/-10) nm]
    • LDH-D-C-440  [laser head (pulsed & CW), wavelength = 440(+/-10) nm]
    • LDH-D-C-485  [laser head (pulsed & CW), wavelength = 485(+/-10) nm]
    • LDH-D-TA-560 [laser head (pulsed & CW), wavelength = 561(+/-3) nm]
    • [~50ps pulse width, repetition rate tunable from 196kHz-40MHz - can measure lifetimes from nsec-μsec range].

    Various dichroic and longpass filters for detection available as needed.

    Objective lenses (Olympus):

    • Plan N 4x, NA = 0.1
    • PL 20x PlanAchromat Objektiv, NA = 0.4
    • PL 40x PlanAchromat Objektiv, NA = 0.65
    • UPLSAPO 60x Ultra-Planapochromat, NA = 1.2 (water immersion)
    • PLAPON 60x  Plan Apo, NA = 1.42 (oil immersion)
    • UPlanSApo 100x, NA = 1.40 (oil immersion)

    Analysis Software:

    • SymPhoTime 64 (see manufacturer website).

    Wikipage by Picoquant to help with TCSPC theory and data analysis.

    Example screen shots for FRET and FCS analysis

    Screen shot from SymPhoTime 64 whilst performing a typical FCS analysis.
    Screen shot from SymPhoTime 64 whilst performing a typical FRET lifetime analysis.

    Another examples


    The principle of Selective Plane Illumination Microscopy (SPIM) consists of illuminating/exciting the studied sample from an axis perpendicular to the imaging axis. This ensures that only the imaged plane is exposed to illumination/excitation light and thereby illiminates out of focus fluorescence and excitation light scattering, while also significantly reducing the effects of phototoxity/bleaching over an entire volume imaging cycle. It thereby facilitates in vivo 3D volume imaging over long periods also for thick samples. An added benefit of SPIM is that since it is a widefield imaging technique, when combined with state-of-the-art sCMOS cameras, volume imaging rates that are orders of magnitude faster than with confocal point scanning microscopy can readily be achieved.

    Unique to the L-SPIM is it’s geometry: The illumination/excitation objective (NA up to 0.5, air) is used to produce a (~1kHz) digitally-scanned light-sheet in the horizontal plane. The detection objective (8mm working distance, NA 0.95, designed for Scale AS (Scaleview A2 clearing, refractive index n~1.38) - like immersion media) is mounted on a standard inverted microscope frame and images from below (vertically). A correction-collar allows for effective use with media/samples with n=1.33-1.38. If you are using higher refractive index clearing methods please contact us regarding the possibility of using a different suitable objective lens.

    Samples are mounted in/on custom sample holders which are immersed in a small bath. The light-sheet is incident through a quartz plate on the side of the bath, whereas the imaging objective enters the bath from the base through a suitably sealed opening. When used with our custom "Plant Holder" (see below), this configuration allows for clean cross sectional imaging of roots  and high resolution 3D mapping of intracellular dynamics for extended periods during growth. On the other hand using our "Slanted Coverslip Holder", allows for fast 3D volume imaging of cleared organs and small, or the early-developmental-stages of, different model organisms (e.g. C. ElegansZebrafish, etc.) that can be mounted directly or indirectly onto the slanted coverlip. The Slanted Coverslip Holder also is also invaluable for routine callibration studies.

    Built into the imaging path is a 3-step changable magnifying optics module which allows for adjustable (optical) magnification of the image on the camera. On the other hand a motorized iris in the light sheet path allows for adjustment of the effective NA of the light sheet (and thereby the light sheet thickness and on-axis uniformity). By careful adjustment of the imaging and lightsheet parameters one can realize an optimal configuration that matches the desried level of detail and field of view for a given study. 

    The sample holder is in all cases mounted from the top to a long travel range single-axis Piezo (travel range 0.8mm), which is translated to acquire volume images. The piezo stage itself is mounted to 3 DC-motors (travel range 2.5cm) which can also be controlled by a joystick to quickly locate regions of interest.

    A custom written user-friendly acquisition software interface (developed in collaboration with Marek Suplata in the group of Katrin Heinze at the University of Wuerzburg), allows for easy control of all imaging parameters and volume acquisition functions, as well as setting arbitrary time-lapse imaging cycles at selectable regions of interest.

    Currently the setup is equipped with 4 excitation laser lines (405nm, 491nm, 515nm and 561nm), and images are acquired on a sCMOS camera (Hamamatsu Orca flash 4.0) capable of 100 frames per second.


    Plant Sample Holder & Plant Box: The Plant Sample Holder is optimized for growing Arabidopsis seeds. The Plant Box allows for programing the local lighting conditions (e.g. to mimic day-night cycles), local temperature variations (via an in-line heater), bath water level control and regulation (via a persitaltic pump and sensor), and automized admisnistration of chemicals to the sample at pre-programmed times as desired (via a micro-needle).

    The Plant Box gives users the ability to study the effect of various physical and chemical perturbations to cellular and developmental processes in plant roots.

    For additional questions regarding technical details / current features of this instrument please contact us at 

    If you are working with plants you may also be interested in the following services.

    Widefield Epi-illumination/detection fluorescence image of Arabidopsis root tip
    Selective Plane Illumination Microscopy (SPIM) image of the same root tip

    Brillouin Scattering Microscope (BSM)

    A key feature of our BSM is the VIPA (Virtually Imaged Phase Array) [1] based spectrometer, which allows one to measure the Brillouin spectral shift with a high efficiency and resolution [2]. By fitting the position of the Brillouin peaks at each scanned pixel one can map the hypersonic velocity and viscoelasticity parameters in a sample.

    In our setup, samples are mounted on an inverted microscope using a custom holder fixed onto a xyz piezo (340μm travel range) which is in turn attached on a joystick controlled DC motor stage. The Piezo stage translates the sample in order to render large area 2D or 3D spectral maps.

    A single longitudinal mode λ=532nm laser is used for excitation, and the back-scattered light is focused through a pinhole (adjustable 50-150μm) to assure confocality before being sent via a dichroic mirror to a grating-based spectrometer or PMT (for Raman scattering or fluorescence detection) or the VIPA spectrometer (for Brillouin spectroscopy).  

    A CCD camera attached to a second port of the microscope frame allows simultaneous widefield imaging, which is useful for locating regions of interest. Widefield epi-illumination or transmission are both possible through either the back-port of the microscope frame or the microscope tower. We have also attached optional DIC prisms and polarizers for the transmission light-path so that one can also obtain DIC images when inserting a slider into the widefield imaging beam path.

    Control, acquisition and analysis are performed via a user friendly Matlab GUI, which allows one to adjust all relevant acquisition and processing parameters. The program can also perform real-time image processing, (re-scaling, alignment and clean-up of spectra followed by non-linear least square fitting) to yield elastic Moduli for each pixel while one is scanning. To simplify imaging workflow the user interface features several standard routines (e.g. time-lapse single point acquisition, lateral xy-scan, axial scan and volume scan).

    For more details and questions regarding technical details / current features of this instrument please contact us at

    [1] M. Shirasaki, FUJITSU Sci. Tech. J. 35(1):113-125 (1999)

    [2] G. Scarcelli and S.H. Yun, Nat. Phot. 2:39-43 (2008)

    If you are working with plants you may also be interested in the following services.



    Instrument Credit Point (ICP) Policy

    Developed or purchased instruments generally follow the "Instrument Credit Points" (ICP) strategy described below.

    The ICP policy is a means by which users can purchase user rights to an instrument (called ICPs). Doing so results in them paying strongly reduced user fees, allows them to obtain priority access to the instrument for a guaranteed amount of time, and gives them prioritized rights to propose modifications and additions to an instrument as their research needs evolve. 

    The VBCF itself typically also holds a limited number of ICPs for any instrument, which guarantees that, in line with our interest of catering to all potential users, the instrument is available to all interested users.

    The possibility of an ICP holder purchasing an instrument "out right" (100% of ICPs) or requesting a duplicate of an instrument for their own lab or facility is possible, however for the former case agreement by all ICP holders as well as approval by the VBCF Advanced Microscopy User Committee (UC) is required.


    Prior agreements

    We attempt to bring projects initiated prior to this date in line with this strategy while still respecting any prior agreements which were made and which were inline with the policy at the time. The terms presented in this document are however in effect since January 1st 2014.

    The general principle of the ICP policy has already been successfully implemented for the purchase of a 3D Structured Illumination Microscope (IMP/IMBA/GMI = 50 ICPs and VBCF = 50 ICPs) and a Fluorescence Lifetime Imaging Microscope (MFPL = 50 ICPs and VBCF = 50 ICPs).

    Project Workflow


    The typical work flow for developing a new instrument is as follows:


    Phase 1:

    Project conception / pioneering studies

    (a) We scout for potential instruments that we believe are viable and beneficial to several research groups.  This phase may also involve pioneering experiments with consumables and equipment we have in the lab.

    (b) People are welcome and invited to approach us with ideas and suggestions.


    Phase 2:

    Presentation 1 / Assessment of potential popularity and interest

    (a) We present the basic concept in a short lecture for which we invite all interested research groups and companies on campus (as well as other institutes and companies on our mailing list).

    (b) All attendees may be asked to fill in a questionnaire after the the presentation, the purpose of which is to assess the instruments potential need and financing.

    (c) Those who could not make the lecture but expressed an interest can be provided with a brief summary of the technique and also invited to fill in the questionnaire.


    Phase 3:

    Detailed Cost & Time Analysis / Prototyping

    If the questionnaire results suggest interest in and financing of the instrument is feasible, we perform an internal Development Cost & Time Analysis (DeCoTA) for the most desirable instrument based on results from the questionnaire - see definition below. At this stage we may also perform additional pioneering experiments and develop basic prototypes using R&D equipment in our lab.


    Phase 4:

    User Committee Feedback / Design Modifications / Agreement on VBCF Contribution

    A UC meeting is called, in which the DeCoTA is presented (which includes estimated ICP costs, timeline and design details that have been determined). It is decided by agreement the maximal and minimal number of ICPs that the VBCF AdvMicro should contribute. If an agreement on this cannot be reached these numbers are decided by the VBCF managing director.


    Phase 5:

    Presentation #2 / Sale of Shares

    (a) Ahead of the final presentation all those who requested for the DeCoTA in the questionnaire are sent a copy. A short non-technical summary is also sent to all those who filled out the questionnaire.

    (b)  All people receiving the DeCoTA are strongly encouraged to contact us personally with any questions prior to the second presentation.

    (c) In a second presentation we present the DeCoTA and answer any further questions.

    (d) Immediately following the presentation, ICPs may be purchased by email. The minimum number of ICPs agreed in the UC meeting are reserved for the AdvMicro VBCF. 


    Phase 6:

    Instrument development

    The instrument is developed or purchased as stated in the DeCoTA document.


    Phase 7:

    Presentation & Demonstration of Instrument

    The instrument is presented in an “opening ceremony” in our lab. The instrument is demonstrated with several test samples provided either by users or by ourselves. At this point also if the instrument functions as stated in the DeCoTA document, the respective ICP holders are sent invoices, the payment of which is due within 2 weeks of receipt. Training sessions and reservations can subsequently be made through our online booking system.





    Development Cost & Time Analysis (DeCoTA)

    This includes the cost for:

    (a) all the components required for the instrument

    (b) Personnel costs for the instruments development

    (c) projected maintenance costs including consumables for two years from the expected completion date of the instrument.

    The DeCoTA folder also includes:

    (a) a description and motivation for the instruments development.

    (b) the projected time-line for the instruments development

    (c) expected user training cost




    (a) Only 100 ICPs are issued for each instrument.

    (b) ICPs can only be requested in units of 10 ICPs (e.g. 10, 20, 30 etc.). Smaller increments are only possible if more than 100 ICPs are requested in total (see below).


    ICPs and Usage

    An ICP entitles you to free usage of the instrument for the numerically equivalent percentage of the total operational hours, calculated on a quarterly basis. Each quarter is considered to consist of a maximum of 540 operational hours (9 hours per day x 5 days per week x 4 weeks per month x 3 months per quarter).

    This arrangement is valid for a period of 2 years following the operational starting date of the instrument. If the operational lifetime of a machine is shorter than 2 years, ICP-holders will receive “ICP credit” for future projects with a value corresponding to the fraction of the remaining 2 year period.

    Usage exceeding your ICPs will be charged at an hourly rate calculated as three times the ICP unit price which the usage time corresponds to (see example below).


    ICPs and Training Fees

    For every 10 purchased ICPs you are entitled to free training of 1 user per year on the instrument.


    ICPs and Access/Booking

    As an ICP holder you have guaranteed access to the instrument for at least the percentage of operating hours each quarter that numerically corresponding to the number of ICPs you have.

    All reservations are made through our online booking system. As an ICP holder you have booking priority over regular users. You can make bookings up to two months in advance. Non-ICP holders can book up to 1 week in advance. Available (unreserved) times may be booked by the VBCF for other users 3 or less days in advance.

    Groups or institutes may collectively buy ICPs, in which case they act as single entities.

    We, the VBCF Advanced Microscopy, can not buy back ICPs (since the money has been invested in the instrument). However, if the lifetime of an instrument is less than the stated 2 years, ICP holders will be compensated for the remaining time (see above). We may under certain circumstances sell some or all of our ICPs for an instrument after its development, to e.g. raise capital for new instruments, or to cater to new research groups. In such cases approval (by vote) of the UC, and final approval by the VBCF managing director needs to be obtained.


    Upgrading/remodeling/adapting of instruments

    After the instrument ICPs have been sold, the hardware costs of any additional modifications to the instrument desired by a research group can rarely be funded entirely by the VBCF AdvMicro. If an ICP holding research group or institute decides they would like to purchase a modification/upgrade for the instrument (e.g. additional laser, objective lens, camera, etc.), we will assist in installing these free of charge. The installation or modification has to be approved by the other ICP holders. If no agreement is reached the UC votes. It is also possible that the upgrade is proposed to all ICP holders, such that each ICP holder contributes e.g. a fraction corresponding to the number of ICPs they respectively own for the instrument.



    If the DeCoTA cost for an instrument comes to 100k EUR, each ICP costs 1k EUR (1%).

    Person “A” buys ICPs for 20% (in the value of 20k EUR), entitling them to 108 free user hours per quarter for the next two years assuming the instrument is projected to run at full capacity. They can reserve the instrument for up to two months in advance, and can train two people for free. After the first quarter it turns out that they used 120 hours (more than planned). The excess 12 hours are charged at a rate of: 3 x 100k EUR / (4320 hrs for 2yrs) = 69 EUR per hour, or 830 EUR (whereas the first 108 hours were effectively charged at only 23 EUR per hour).

    For comparison, if person “A” had not purchased any ICPs they would be charged 8.3k EUR that quarter alone! If they had comparable usage for 2 years this would amount to 67k EUR plus any additional costs for training and consulting. They could have saved almost 50k EUR over the course of 2 years if they had bought ICPs.


    ICP acquisition rules

    ICPs may be requested initially for 2 weeks following the second presentation. Within these 2 weeks no individual or entity can ask to purchase more than 50 ICPs of a given instrument. If collectively over 100 ICPs are requested after this time, the granted ICP numbers are re-normalized. This means that if e.g. both person 1 and person 2 request 50 ICPs each, and the VBCF Advanced Microscopy minimum self-purchased amount is 10, then each person only receives 45 ICPs (so that their contributions remain equal relative to each other, whereas the contribution of the VBCF towards the entire instrument remains unchanged).

    If 2 weeks after the initial offering 100 ICPs have not been claimed (even if the VBCF Advanced Microscopy Facility offers its maximum stake), all parties are allowed to request additional ICPs (>50). The project is also at this stage advertised to interested outside parties (such as the ISTA, TU, Uni-Vienna, BOKU, etc.). In the event that the 100 mark is not reached after two weeks the UC is called to vote on whether to:

    1)      extend the ICP offering time

    2)      drop the project

    3)      (if possible) pursue the development of a stripped down (reduced cost) version

    4)      increase the maximum amount the VBCF Advanced Microscopy contribute to the project.

    In the case of (3) all interested parties are informed and asked to re-asses whether they would still be interested in purchasing ICPs for the modified design.


    2 years after Instrument Introduction

    The fate of a given instrument after 2 years largely depends on its “popularity”.

    If it is clear that the instrument is still in use by numerous research groups, the instrument is maintained in the lab and all parties can reserve the instrument at a nominal user fee. The user fee is re-calculated from the maintenance and running consumables cost for the instrument. An additional personnel fee also applies for training.

    If there is uncertainty whether the instrument will prove useful, the UC is called to vote on whether the instrument should be kept or disassembled for parts. However, it will be guarantied that any ongoing research project of an ICP holder reliant on the given instrument can be finished before the instrument is set out of operation.

    If any instruments usage falls below 15% for two consecutive quarters we maintain the right to disassemble the instrument for parts.


    Special Cases

    If after no less than 3 months after the instrument is operational a research group or institute decides that they would like to out right purchase the instrument the request may be granted under one of the following conditions:

    (a) Unanimous UC decision

    (b) 3rd party access to the instrument via VBCF is granted (the fraction of which is agreed by the UC)

    (c) The interested party requests and commissions a duplicate of the instrument (either for themselves or to be kept at the VBCF).


    If you are not an ICP holder

    You can still use the instrument at a rate that is charged hourly and equal to three times the ICP price that the usage time constitutes to the 2 year period (8 quarters x 540 hrs = 4320 hrs). This rate is equivalent to the "excess hour" charge for ICP holders.

    Unlike an ICP holder you are not guaranteed to have access to the instrument at the times you request - you can only make reservations the same week.

    Additional training and consultation costs apply.

    If you are a new group leader at one of the institutes at the VBC, advMICRO VBCF will offer to sell you ICP of existing instruments (subject to availability).

    Instrument Credit Points

    Funding for instruments is achieved in the framework of our "Instrument Credit Points (ICP) Policy", which allows users to reserve free usage rights to an instrument at a strongly reduced rate prioir to instrument development. ICPs can be reserved following the open seminar presenting the planned instrument and are only charged once the instrument is shown to be operational (according to benchmarks described in the presentation). Hence there is no risk that the instrument will not as stated.

    Users who have not purchased ICPs are ofcourse still eligible to use the instrument, however they no longer receive the special reduced rate as well as several other advantages (see above). 

    The idea of ICPs is quite simple and can probably be best illustrated by example. We firstly calculate the complete subsidized devlopment and maintenance cost of an instrument for it's expected useful lifetime, say this comes to 200k EUR for two years. If a user offers to pay 20% of this (40k EUR), which corresponds to buying 20 ICPs, they will be eligible to 20% of the operational hours of the instrument for two years at no extra charge (no invoice). Operational hours are calculated as 9 hrs per day 5 days a week. This particular user would then be eligible to 216 free hours over two years (or on average ~7 hrs per month). Ofcourse they can use the instrument more (subject to the availability of the instrument), however they will then be charged the "regular user fee" per hour, which is more expensive. It thus makes sense to purchase ICPs according to what you expect your usage time of an instrument will be. The more ICPs you have the more significant your consideration for proposed extensions/modification to the instrument will be.

    The full ICP policy can be found under the following link.

    You may also download a PDF of the ICP policy here.

    Frontier in Optics & Microscopy Lecture Series

    A set of talks by leading microscopists from around the world hosted at the Vienna Campus Biocenter by VBCF-Advanced Microscopy. Everyone is invited to attend these talks. If you are not affiliated with the IMP, IMBA, GMI or MFPL please send us a quick email at stating which talk(s) you are planning to attend.


    IMP Main Lecture Hall, Dr. Bohr Gasse 7, Vienna A-1030

    Unless stated otherwise all talks start at 11am (talks typically last 30min to 1 hour)

    27th July 2016

    Jörg Enderlein (Georg-August-University Göttingen, DE)

    "High- and Super-resolution Fluorescence Microscopy"

    28th June 2016

    Monika Ritsch-Marte (Medical University of Innsbruck, AT)

    “Advanced optical wavefront shaping for holographic trapping and imaging”

    20. November 2015

    Pavel Tomancak (Max Planck Institute of Molecular Cell Biology and Genetics, DE)

    "Guide to Light Sheet Microscopy for Adventerous Biologists"

    29. July 2015

    Peter Török (Imperial College, UK)

    "High numerical aperture microscopy and some unusual applications"

    23. April 2015

    Eric Betzig (Janelia Farms, USA)

    "Imaging Life at High Spatiotemporal Resolution"

    15. October 2014

    Tony Wilson (Oxford University, UK)

    "Making Light Work in Microsocpy"

    16. April 2014

    Gerhard Schuetz (Vienna University of Technology, AT)

    "Single Molecule Microscopy to Study Dynamics & Associations of Plasma Membrane Proteins"

    26. February 2014

    Hari Shroff (NIBIB/NIH, USA)

    "Faster and Sharper: New Technologies for 4D Imaging"

    15. January 2014

    Alberto Diaspro (Istituto Italiano di Tecnologia, IT)

    "Super Resolution Portrait of Cells at Nanoscale"

    23. October 2013

    Giuliano Scarcelli (Harvard University, USA)

    "Brillouin Microscopy For Tissue Biomechanics"

    FLIM/FCS Workshop

    Together with MFPL and Picoquant we will be organizing a 3rd FLIM/FCS Workshop in Vienna on the 18th & 19th November 2014.

    We have a great line-up of confirmed speakers and several hands-on workshops scheduled. The scope of the workshop, as in previous years, includes all biological & biomedical applications of, aswell as technical innovations related to time-resolved fluorescence imaging and spectroscopy.

    Official CSF workshop page:



    Looking back: last years FLIM/FCS Workshop

    On the 12th & 13th of November 2013,  the MFPL, Picoquant GmbH and CSF Advanced Microscopy succesfully organized and hosted the...

    2nd Max F. Perutz Laboratories FLIM & FCS Workshop

    (PDF flyer)

    The event was free and open to everyone interested, and attracted more than 50 participants from 6 countries. Free demo sessions on our FLIM/FCS microscope (Picoquant) and 3d Structured Illumination Microscope (OMX, Applied Precision/GE) were given on both afternoons. Based on feedback the workshop was considered a big success and we are looking forward to co-organizing a 3rd installation next year.

    The schedule for the workshop was:

    12 Nov. 2013 (IMP Lecture Hall, Dr. Bohr-Gasse 7, Vienna 1030)

    09:00 - 09:30 Ivan Yudushkin (MFPL) - "FLIM for biologists: a showcase"
    09:30 - 10:00 Gerhard Schütz (TU Vienna) - "Tracking single molecules in the live cell plasma membrane"
    10:00 - 10:30 Kareem Elsayad (CSF) - "Getting and making the most out of fluorescence lifetimes"
    10:30 - 11:00 Coffee break
    11:00 - 11:30 Sofia Johansson (Karolinska) - "Dynamics of Natural Killer cell receptors and ligands at the cell surface"
    11:30 - 12:00 Felix Koberling (PicoQuant) - "Current concepts for time- and polarization-resolved fluorescence imaging"
    12:00 - 13:00 Lunch (IMP cafeteria)
    13:00 - 17:00 Demo sessions*
    17:00 - 18:00 Open discussion / social event (VBC5 - Lecture Hall B)

    13 Nov. 2013 (MFPL, Rm. 6.506, Dr. Bohr-Gasse 9, Vienna 1030)

    09:00 - 09:30 Katrin Heinze (University of Würzburg) - TBA
    09:30 - 10:00 Gottfried Köhler (MFPL) - "Is virus uncoating directional? An example for use of FCS"
    10:00 - 10:30 Susanne Trautmann (PicoQuant) - "An introduction to advances in fluorescence correlation spectroscopy (FCS): application and technology"
    10:30 - 11:00 Coffee break
    11:00 - 11:30 Edmundo Sanchez Guajardo (CSF) - "Microscopes at the CSF: current and planned"
    11:30 - 12:00 Ivan Yudushkin (MFPL) - "Design of FRET probes"
    12:00 - 13:00 Lunch (IMP cafeteria) - 13:00 - 17:00 Demo sessions*
    17:00 - 18:00 Open discussion / social event (VBC5 - Lecture Hall B)

    Interested in doing an internship/Praktika in Advanced Optical Microscopy?

    We have several optics & programming projects available including:



    Suitable for Biology/Biomedical students

    - Diagnostic applications of low-frequency light scattering spectroscopy (1-6 months)

    - Correlated Brillouin Scattering and Mass Spectroscopy Imaging (1-6 months)



    Suitable for Electrical Engineering / Computer-science  students

    - Development and optimization of Instrument Control/Automation and user interfaces (1-6 months)

    - Implementation of Compressive sensing algorithms (3-6 month)



    Suitable for Electrical engineering (EE) students

    - Ultra-fast multi-scale time-resolved spectroscopy (3-6 months)

    - Novel high resolution Light Sheet Microscopy (3-6 months)



    Suitable for physical-science/mathematics students

    - Multi-scale correlation analysis (3-6 months)

    - Intelligent spectral pattern matching algorithms (3-6 months)


    For projects involving programming skills experience with Matlab or lower level languages is desirable.



    Please send inquiries with a CV to



    FEMtech Funding?

    If you are currently doing your Masters in Austria and are female, you are eligible to apply for a FEMtech fellowship. FEMtech fellowships provide a generous stipend for 1-6 months to work on specific research or development projects within the facility. Please contact us for further details at:

    Further information on FEMtech funding can be found here: