Biomedical image data can be produced by different instruments. In hospitals the most frequent source of such data are computer tomography (CT) of the brain, magnetic resonance imaging (MRI), ultrasound imaging or X-ray imag-ing. For research purposes, however, the most frequent instrument is an optical microscope (typically cells or their components are stained, observed in a fluorescence microscope, their image is recorded using a CCD camera, trans-ferred to computer memory and analysed by computer). Analysis of biomedical image data is a good example of a problem that needs collaboration of experts in biology, mathematics and computer science (or experts with knowl-edge in all these disciplines). In the case of optical microscopy also expertise in physics (optics) is an advantage. An example of a laboratory that attends to the analysis of biomedical image data acquired using optical microscopy and that gathers experts in the above-mentioned disciplines is Laboratory of Optical Microscopy at Masaryk University. This paper summarizes scientific problems solved in this laboratory.