For certain stems cells, there are cell surface markers (cluster of differentiation; CD) that can also be used to track down these cells, either with flow cytometry or other monoclonal antibody/fluorescence-based assays. The problem is that the stem cells are usually very rare and thus difficult to detect, and in many cases the CD markers are not well defined. But if you have a cell and want to know if it is a stem cell, then you can try staining it with fluorochrome-labeled antibodies for certain CD markers and check it out e.g. with a confocal laser microscope. Or if you have many cells, run them through a flow cytometer.