I'm having an issue where I follow the instructions on the "Calibrate XY" menu of the HCS Site Generator plugin, but instead of applying an xy offset, no calibration takes place.
The red square representing where the plugin thinks the stage is relative to the plate simply moves corresponding to the magnitude of the xy correction. Double clicking on the well diagram to move the stage confirms that the calibration did not take place - there's still a small (half a well) offset between the where the plate really is and where uManager thinks it is.
I've tried restarting the microscope, restarting uManager, and running calibrating the stage using "Set Origin" from the Stage Position List menu. Nothing helps.