Abstract: An apparatus 20 for the separation of a subpopulation of cells from an intact organ or other biological material is provided. The apparatus 20 includes: (1) a digestion chamber 24 that integrates the primary digestion process, (2) a measuring cylinder 26, (3) a cell collection chamber 28, (4) a heat exchanger 30 for raising and lowering temperatures in the digestion chamber 24 to activate or inactivate enzymes, (5) sensors 112, 114, 116, 118, 120, 122 to complete a closed feedback loop for allowing optimization of the digestion process, and (6) mock cells which mimic the cells to be harvested and which are used to fully optimize the process without unnecessary destruction of harvested cells. The manipulation of the digestion process may be manual or may be automated under computer control.