I'm not expert but used FP for long, auto-fluorescence can be measured during baseline recording (put fiber tip stable in air) in dark environment with a reference channel (e.g. one optic input + one empty electric input), delta F should remain constantly small. I don't know the exactly threshold but you should not see any obvious spontaneous response. In some dirty or broken fibers, auto-fluorescence can be huge, even bigger than real calcium signals. I recommend use Doric low-auto-fluorescence fiber cord to avoid those troubles. (Some say bleaching the fiber for hours before rec can reduce auto-flu, but I tested the effect is very limited) You're correct about the fiber core size and NA value, it's the most common used parameter in FP, 400um gives 4 times more fluorescent signal than 200um core and bigger NA value helps to capture wider range signal below fiber tip. Though I recently got to know it's not necessary to use the same NA value in patch cord, only necessary of implanted fiber cannula. Hope helps.