Factors to be considered for the success of microscopy-based projects: The development of highly specialized microscopes has improved the quality of raw data in image-based projects. However, optimal results are based on the choice of adequate imaging systems. A complete overview of available imaging technologies is beyond the scope of this review. However, as a guideline, the choice of an adequate microscope is based on sample- and project-specific factors. The optics of the microscope need to acquire images with adequate resolution and penetration depth, and a level of acceptable phototoxic stress needs to be considered for the illumination of the sample. At the level of project management, the needed throughput, which tends to be high in systems biology, needs to be considered, and an adequate image analysis infrastructure needs to be in place to avoid bottlenecks in image analysis and the interpretation of data.