During this step the software creates and applies a flat to pre-correct the images as they’re being saved. The incident laser line that forms a sheet after passing through a cylindrical lens has a Gaussian profile, and the flat corrects for and "flattens" the intensity of the field of view. Warning: this step is not easily reversible, because the flat is applied to the saved data.
The SmartSPIM software, using TerraStitcher, generates a single, 2D, stitched plane image of the whole brain (typically 20-28 tiles). There are six sliders to adjust the brightness (Display Range), the amplitude and center of the tile-overlap adjustments (L amp, L center, R amp, R center), and the L/R brightness (Left/Right Balance). Adjust both the left and right hemisphere to create a clean “corrected” image. The “raw” or “original” image is pictured on the left, and the corrected image is on the right.