This protocol can be applied to any strain of cell that can be safely run through a flow cytometer. For clarity, we have written it assuming E. coli DH5-alpha; to apply the protocol to another cell type, substitute the other cell type for any place where the protocol says [E. coli DH5-alpha]. This protocol has been written for measurement of GFP, YFP, or other yellow/green fluorescent proteins into MEFL units. To apply it to fluorescent proteins of other colors: Replace BBa_J364001 with a construct for strong expression of the other protein. For blue proteins (e.g., mTagBFP), measure with 405nm excitation and 450nm/50nm emission filter. Units will be MEC30. For red/orange proteins (e.g., mCherry), measure with 561nm excitation and 610nm/20nm or 620nm/15nm emission filter. Units will be MEPTR. For far-red / near-infrared proteins (e.g., IRFP), measure with 635nm excitation and 780nm/60nm or 750nm long-pass (LP) emission filter. Units will be MEAPCY7. To apply the protocol to multiple colors, add a positive process control for each color and use one of the tools on the iGEM Measurement Resources page to compensate measurements for spectral overlap. This protocol can be combined with bead-based cell size calibration.