07.0 Alignment

Alignment

Aligning the scan can be carried out through the following code and following the GUI. Alignment can only be done of the Fluorescence images or the Region of Interest images set in the setup_det_chan() function. User will define which one to use in the GUI. Once all alignment centers have been set, it is ok to just quit out of the windows.

test_fs.alignment(reset=False)

reset (bool) - if you would like to completely reset the alignment make this equal True

• if you import new scan numbers you must make sure reset=True for the first alignment