Improvements to Part I
significant speed up; switched to third-party tiff loader and writers; A big improvement also come from moving the frame index to the third position i.e. tif_stack(row,column,frame) not tif_stack(frame,row,column) This way each frame is contiguous in memory and makes alignment, etc step faster. It also matches better how tiff are stored. It also means most uses of squeeze are unnecessary e.g. mean_phase=mean(fov.phase,3) (no squeeze)