If it was me, I would first amplify the signal with an instrumentation amp, and perhaps filter the signal with a high pass filter (perhaps followed by more amplification). I would then use an external comparator (or find a PIC with one inbuilt) and add some hystersis, this should be easily done if your signal is now in order of hundreds of millivolts or more.
Use a DAC or potentiometer to set the threshold (DAC would be nicer, you could make an algorithm that hunts for a typically valid range of count values), others in this thread have discussed internal PIC comparators.
Feed the output of the comparator into a Timer clock. On another timer, set it to generate interrupts every second (or time period of interest). On every interrupt, read the value of the externally clocked timer, reset it 0, and update the count value as displayed on the LCD, or output a new value over serial or whatever.
If you are trying to discriminate or sample a signal in the order of 1 millivolt, your gonna have a bad time! Google ECG instrumentation amplifier, it should start you down a proven path that others have taken.