The services offered by the BioOptics Facility to researchers at IMP, IMBA and GMI cover analytical flow cytometry and cell sorting, as well as a large variety of microscopy techniques, image processing and analysis.

Flow Cytometry

We provide instrumentation, education and expertise for all flow cytometry requiring experiments, and offer high-speed cell sorting as well as advanced and general flow cytometry analysis. Users are given guidance and support with the planning of experiments and implementation of new fluorophore combinations. They are trained in the use of hardware and software for all of the available state-of-the-art flow cytometers (analyzers and sorters), as well as in data processing and analysis. Three BD Aria cell sorters are operated by the staff of the facility to sort up to four cell populations simultaneously in bulk, or conduct single cell sorting.

If you have questions please contact facs(at)

For sorter bookings please use the JIRA Service Desk.


The BioOptics Facility currently manages more than thirty microscopy systems, including wide-field microscopy, confocal laser scanning microscopy (CLSM), two-photon (2P) microscopy, total internal reflection (TIRF) microscopy, structured illumination microscopy (SIM) and light-sheet fluorescence microscopy (LSFM) techniques as well as automated slide scanning for samples with or without fluorescence. Most of the systems are motorized -, thus providing automation for higher throughput, - and are suitable for both fixed samples and live cell experiments. The facility provides assisted use and training on all instrumentation and consultation concerning all microscopy-related subjects, including project planning, staining, microscope selection, etc. Additionally intense basic as well as advanced practical microscopy courses are organized including hands-on sessions as well as lectures by internal and external faculty.

If you have questions or have another request please contact microscopy(at)



Image Processing and Analysis

At the BioOptics Facility we provide several state of the art workstations, equipped with commercial software as well as freeware products for image processing, analysis and visualization. For the deconvolution of microscopy images we deploy two machines with high-end GPUs and terabytes of RAM to enable processing of large datasets.

We provide training for the use of specific software, depending on their demand, as well as a more general introduction to image analysis during monthly theory sessions. Typical analysis tasks would include object tracking, neuron tracing, cell segmentation in 2D and 3D, measurement of intensity, area and volume as well as co-localization.

For advanced image analysis and automated processing we provide customized scripts and tailored workflows, facilitating ease of use and reproducibility of data creation

If you have questions or another request please contact image.analysis(at)