The beautiful thing is we do not align timepoints in the traditional sense, there is no need to modify your original .tif image files.
Alignment is done by specifying a ‘pivot point’ that is common to all timepoints to be aligned.
Fitting tube diameters
Tube diameters are fit as threshold crossing at the full width at half maximum (FWHM).
Sliding maximal z-projection
This is used to visualize slices above and below the current imaging plane. Please see my main website, here, for more information.