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.