I’m taking 2 and 3 color STORM images of my samples and I’m facing a problem how to register the channels properly. Cross-correlation drift correction works just fine within each channel but does not take into account the interchannel drift or chromatic aberration. Due to our microscope setup, I have to always record one channel first and then move to the second one once the first one is finished (so not alternating between the channels). Due to these reasons I’ve ended up using fiducial markers (TetraSpeck). However, I still haven’t found a way to register channels with the fiducials. It seems that ThunderSTORM does not have such a property (?) and haven’t found any other plugins either capable of doing this. I’m sure some tools must exist since there are so many multi-color STORM papers but the papers typically don’t report these details. Could anyone help me with this registration issue?