Within each section directory you will find the image files. If you are using ScanImage for the acquisition and doing tile-scanning (grid of images) then each TIFF will contain all depths from all channels for each x/y position. So if you have a 3 x 3 tile grid, there will be 9 TIFFs per section directory. Once all tiles have been acquired, an empty file called
COMPLETED is added. There is also a file called
tilePositions.mat, which contains the position of each tile in the grid (including the stage coordinates reported by the stage). This file is created by the callback function
SIBT.tileAcqDone which in a tile scan runs at the conclusion of each X/Y position.