Hilary,

Frames are not replaced in CONN.  CONN only accounts for the spikes and includes them as nuisance in any estimation models.  As for how to account for the total number, I'm not certain if there's an output somewhere in the pipeline, but one could simply count the spikes in the GUI Denoise tab window.  If you run your pointer across the spike graphic, it will show you "0" values along the time course where spikes were detected based upon your ART threshold.

Warm regards,
Jeff