If you would like to convert the multi-position images obtained with the two-photon microscope (TriMScope) to 3d OME stacks run the script Trimscope2OMEStack (can be found in \\CAIC-1\Public\Software\MatlabScripts).
You will need the folder bfmatlab: either you run the scripts directly from \\CAIC-1\Public\Software\MatlabScripts (you don't need to do anything) or you uppdate the line
addpath '.\bfmatlab'
with the location of the bfmatlab folder on your computer.
The script will request information on pixel size in X, Y and Z, the folder with the input images and the folder where you want to store the results.