Described herein are various systems, methods, and apparatus for systematic creation of isolated homogeneous colonies of cells from vector-based lineages. The vector-based lineages may originate from multiple types of viral vector families (e.g., Paramyx-oviridae, Retroviridae, Parvoviridae) or non-natural engineered vectors or a plurality of vector combinations, for example. In certain embodiments, the isolated homogeneous colonies of cells are vector-free sub-colonies; in other embodiments, the isolated homogeneous colonies of cells are homogeneous vector sub-colonies. In other embodiments, vector mixed sub-colonies are created. The disclosed systems, methods, and apparatus are useful for inducible pluripotent stem cell (iPSC) production and work by selectively binding to one or more corresponding protein markers expressed on the surface of a cell that indicate that cellular reprogramming has occurred. Software is used to automate the purification and isolation of the iPSCs produced.