Creating an atlas is more encompassing than image acquisition and analysis. It requires a clear understanding of the biological questions to be addressed. Then appropriate labeling, sample preparation, imaging, image analysis, visualization, and data management methods must be selected (Figure 2). An interdisciplinary team is required that collectively possess the needed expertise. Generating useful atlases is still in its infancy. Which methods to use at each step along the pipeline will depend greatly on what analysis is required. There is currently no ‘magic toolbox’ that scientists can use to apply to their specific task. Each step has to be tailored to suit the experiment.