We are now at a time when we can systematically alter animals genetically so that any given protein or its expression can be observed in a targeted set of cells. Combined with new modalities of light microscopy, this allows us to observe molecular mechanisms within the cell, observe the developmental trajectory of growing organs, and to map the cellular anatomy of organisms and organs such as a fly brain. Several brief examples from our work will be presented: on the biophysics of cell division, on C.elegans lineage tracking, and on the reconstruction of every neuron in a fly brain. To end, we give a vision of microscopes and software that we hope will lead to an understanding of how complex tissues and shapes develop in cellular terms.