Hello

You have a few choices

1) manually identify the ectopic beats and remove the wayward data

2) manually identify the beats, remove and then interpolate the wayward data

do 1 and 2 with automatic methods.

If you just have just a few recordings then a manual removal will work. IF you have many recordings you will probably need to automate.

@Edward Marcus  Thank you

Are you finding a threshold current before stimulating? Most people use 2X threshold current. You could stimulate at a higher rate to make sure the cells are refractory. 

@Girish, could you please explain what you mean by 'threshold current' ? I always keep the current constant and identical for all isolated heart, but at would like to know more about what you suggested. Thanks 

On second thought, if every stimulus is being captured, then it's unlikely that threshold current is the problem. It might be hard to get rid of the ectopic beats.

Sorry, this is probably too late now, but can I ask you what perfusion pressure you are using? If the heart is hypoxic, it may manifest more ectopy. If you turn off the stimulator after the recording, what is the spontaneous HR? If it's low (150-180), it might be an indication of underperfusion, perhaps?

@Jakub Tomek

I set the heart under a PP between 40-60mmHg. What PP would you recommend?

When stimulator is turned off, the spontaneous HR is quiet variable depending of the heart, but mostly between 200-300 mmHg.

Thanks for your input.