Problem in Z direction when using SMAP calibrations

[cleterrier]

I use a SMAP calibration from -800 to 800 nm (3dcal.mat file from a spline fitting calibration procedure). The calibration goes from low to high (that is simulating Z positions from -800 to 800 nm by moving the stage and beads stuck on a coverslip up through the focal plane on an inverted microscope).

However, when using this calibration file in DECODE, the resulting fitted coordinates are reversed, i.e. the -800 nm is now 800 nm and +800 nm is now -800 nm (sample is "upside down" compared to what it should). It's not that much of a problem (I reverse the Z coordinates at post-processing), but when you use a non-symmetrical calibration or training (say -400nm to +800 nm) it's confusing.

(btw this could be in "Issues" but I'm not sure if it is really an issue)

[Haydnspass]

We plan on changing our coordinate system to the default, it's not really an issue/bug as such because we are consistent internally, but I agree it can be confusing.
Will be changed sometime in the future :P