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.
To adjust the fill fraction use the 'Fill Fraction' controls in the Configuration Panel.
The fill fraction determines the width of the active acquisition over a line. The beam modified line clock is generated by ScanImage to attenuate the laser power during the inactive portion of the scan.
The scan path of the laser beam determines the scan field. The actual image field is only a portion of the entire scan field. The width of the image field relative to the scan field is determined by the Fill Fraction.
