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The PiCapture boards do not use any of the GPIO pins in normal operation – they are all available for your application. The PiCapture “HAT” provides for passthrough of the 40-pin connector so that additional boards can be simply stacked.
If you would like to use the PiVideo software to control PiCapture, then the pins required for the chosen port (serial, I2c0, or I2c1) are used to communicate with the PiCapture processor. The jumpers on the PiCapture boards can be used to connect or disconnect these signals – please refer to the Documentation for details.