External program call

Dear all,

what is the cleanest way to call external program while staying in CP pipeline GUI? I am not aware of any module, I was thinking about passing via imageJ with a macro file containing an external program call, but I hesitate a bit. I am not sure if it change anything but I would call two different things (in two different places of the pipeline) i) shell macro ii) matlab code processing images. Thanks for any hints or advices.

Hi,

CP doesn’t directly have a means to make external program calls. However, this could be done using the RunImageJ module, by using some of techniques suggested here.

Regards,
-Mark