What exactly is the difference between these two parameters? Furthermore, in the One protocol I'm giving three SPAD related vales: PQ SPAD, PQ SPAD1, PQ SPAD2, and PQ SPAD 3 - what is the difference?
We run the SPAD protocol at three different light intensities, and then the macro chooses which of those light intensities give the best answer. This allows PhotosynQ to provide accurate SPAD values, even when leaves are very thin or very thick.
PQ SPAD 1,2, and 3 are the values from the measurement at each of the three light intensities with PQ SPAD 1 being at the lowest intensity and PQ SPAD 3 being at the highest light intensity. The parameter 'PQ SPAD' is the mean of the most accurate measurements. For example, the macro may eliminate PQ SPAD 3 and then use the average of PQ SPAD 1 and 2 to provide the final "PQ SPAD' parameter.
About NPQt and phiNPQ, partly written here: https://photosynq.org/forums/technical-support-and-questions/discussions/difference-between-phi2-phino-phinpq