Automated confocal microscopy: the way of achieving both quality and quantity in 3D image cytometry

Image cytometry is mostly associated with high quality but low quantity, whereas flow cytometry is associated with high quantity but low quality. Achieving both quality and quantity in cytometry is possible in the case of automated confocal microscopy systems. We have shown that the automation of image acquisition and image processing in confocal microscopy is possible for specific tasks such as 2D and 3D FISH imaging. This paper is focused on practical problems and solutions that we have encountered during our research. We believe that our experience might be helpful to all those who decide to automate their light microscopy systems for cell studies, i.e. for image cytometry purposes.