At the very edges of the resonant mirror's scan field the angular velocity of the resonant mirror is low, so that the laser power is attenuated in this region to prevent the sample from burning. Additionally the acquisition is inactive so that no pixels are formed in this region.
The ratio between the length of an active acquisition of a line and the total length of the line is the fill fraction. The fill fraction can be expressed temporally (ft) and spatially (fs) and can be calculated with the formula
ft = 2 * line active acquisition time / scanner period
fs = angle of active acquisition / ( 2 * scanner angular amplitude )
The relationship between the spatial fill fraction and the temporal fill fraction can be expressed as
fs = cos( (1-ft) * pi/2 )
ScanImage generates a beam modified line clock to attenuate the laser power relative to the active acquisition. This clock is used in the Beams module to control the Pockels Cells for fast modulation of the laser beam.