Computer-implemented methods, software, and systems for determining a distribution of neuronal cells across a portion of a brain are described. One computer-implemented method for determining a target distribution of one or more neuronal cells across a portion of a brain, comprising: constraining, by one or more computers, a start distribution of the one or more neuronal cells by expression of one or more marker genes and by protein stain of the one or more marker genes across the portion of the brain to obtain the target distribution.