Analysis of the spatial distribution of endomembrane trafficking is fundamental to understand the mechanisms controlling cellular dynamics, cell homeostasy, and cell interaction with its external environment in normal and pathological situations. The development of automated methods to visualize and quantify the spatial distribution of intracellular events is essential to process the ever-increasing amount of data generated with modern light mi-croscopy. We present a generic and non-parametric framework to quantitatively analyze and visualize the spatio-temporal distribution of intracellular events from different conditions in fluorescence microscopy. From the spatial coordinates of intracellular features such as segmented subcellular structures or dynamic processes like vesicle trajectories, QuantEv automatically estimates weighted densities for each dimension of the 3D cylindrical coordinate system and performs a comprehensive statistical analysis from distribution distances. We apply this approach to study the spatio-temporal distribution of moving Rab6 fluorescently labeled membranes with respect to their direction of movement in cells constrained in crossbow-and disk-shaped fibronectin patterns. We also investigate the position of the generating hub of Rab11 positive membranes and the effect of actin disruption on Rab11 trafficking in coordination with cell shape. An Icy plugin and a tutorial are available at http://icy.bioimageanalysis.org/plugin/QuantEv.