Recently, we have described a high-resolution cytometry (HRCM) technique (Cytometry 36:279-293) as a reasonable compromise between flow cytometry (FCM) and laser scanning cytometry (LSCM) on one hand and confocal laser scanning microscopy (CLSM) on the other hand. Whereas FCM/LSCM and CLSM enable measuring of either large number of cells with low resolution or small number of cells with high resolution, respectively, HRCM can analyze quantities comparable to FCM/LSCM measurements (using overnight acquisition) with an accuracy comparable to CLSM. Very recently we have built a second HRCM instrument (see picture at http://www.fi.muni.cz/lom) which enables switching between conventional and confocal modes. The confocal mode is realized using a 5% Nipkow disk optimized for fluorescence imaging. It offers a better resolution but at a lower speed. The user can choose which fluorochromes are imaged in confocal mode. Thus, the system can be configured for a variety of imaging modes ranging from quick 2-D analysis up to high-resolution confocal 3-D studies.