In the last decades high-resolution microscopy revolutionized not only the scope of biological applications, but also called for suitable adaptations of existing image analysis methods in order to maximize the information that can be retrieved. At the same time, 3D microscopy techniques and multi-color measurements have attracted a lot of attention since they allow for an even broader range and complexity of simultaneous measurements. Through colocalization analysis we can infer on interactions between proteins, cells, and particles to enhance understanding of DNA replication and transcriptional processes.