To understand biological processes it is often necessary to examine the spatial organization of biological objects. Examples are the interaction of molecules, the sub-cellular localization of molecules or the clustering behavior of specific cells. In this workshop we use FIJI/ImageJ and napari to analyze the spatial organization of molecules and cells and to visualize the results in 3D. We make use of a napari-plugin "napari-j" we developed, to easily exchange images and data between napari and FIJI. We measure the distances of objects from a given point or from a given surface, for example the distances of molecules from the center or the membrane of a cell. We also measure the distances of molecules or cells from each other and visualize he results. We use the DBScan clustering algorithms to find densely populated zones in our images. Finally we apply spatial statistics, using the empty space function, nearest neighbor statistics and Ripley's K-function to decide whether the spot co-localization and clustering results we observed are different from those to be expected by chance.