Method and device for automated cell analysis and determination of transport and communication between living cells by analyzing the formation of tunneling nanotubes (TNTs) between cells. This method comprising the steps of singularizing cells in a culture medium and staining the cells with a fluorescent or luminescent dyes for staining of cytoplasm and membranes as well as TNTs, flagella and other cell particles for 3-D cell microscopy. The method comprises further an image analysis system.