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 three available state-of-the-art flow cytometers, as well as in data processing and analysis. Three 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.


The BioOptics Facility currently manages more than twenty 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 lightsheet 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.

Image Processing and Analysis

Five state-of-the-art computer workstations are available at the BioOptics Facility, operating most of the common commercial image processing and visualization software. For the deconvolution of microscopy images, a server solution with a web-based interface has been set up in order to provide efficient, multi-user, parallel, batch deconvolution that can easily be started from the individual scientist’s computer.

Users are trained in the use of specific software, depending on their demands or are trained in an annual course on image processing and analysis with lectures and hands-on sessions by the BioOptics staff. Several image analysis algorithms are available, such as object tracking and tracing, determination of measurement parameters like intensity, distance, area, volume and co-localization.

For advanced image analysis and automated object recognition, customized classification and measuring algorithms are developed within the facility.