vasylvaskivskyi/opt_flow_reg

Optical flow based registration for fluorescence microscopy images

Optical flow based registration for immunofluorescence images

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.

Command line arguments

-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

Example usage

python opt_flow_reg.py -i /path/to/iamge/stack/out.tif -c "DAPI" -o /path/to/output/dir/ -n 3

Dependencies

numpy tifffile opencv-contrib-python dask