These scripts perform fine registration using warping. A map for warping is calculated using RLOF optical flow algorithm, by OpenCV. Although images are MINMAX normalized during processing, optical flow algorithms expect images to have similar pixel intensities.
Currently does not support z-stacks.
-i
path to image stack
-c
name of reference channel
-o
output directory
-n
multiprocessing: number of processes, default 1
####Optional
--tile_size
size of a square tile, default 1000, which corresponds to 1000x1000px tile
--overlap
overlap between tiles, default 100
--method
optical flow method: farneback, denselk, deepflow, rlof, pcaflow, default rlof
python opt_flow_reg.py -i /path/to/iamge/stack/out.tif -c "DAPI" -o /path/to/output/dir/ -n 3
numpy tifffile opencv-contrib-python dask