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Flow-Registration: Optical flow based motion compensation / video stabilization / registration for 2-photon imaging data

Toolbox for the compensation and stabilization of multichannel microscopy videos. The code is written in Matlab, Java (IJ Plugin) and C++. The publication for this toolbox can be found here and the project website with video results here.

Fig1

Installation

To install the toolbox clone the repo or download the most recent release and run the set_path.m script. With savepath the toolbox will be permanently available in MATLAB.

Please contact us for more details.

Requirements

To run this toolbox, MATLAB 2018b onwards with configured C++ compiler (check here for supported compilers) is required.

Getting started

This repository contains the demo scripts demos/jupiter.m and demos/jupiter_minimal_example.m which run out of the box and compensate the jitter in an amateur recording of a meteor impact on jupiter. The folder demos/examples contains examples that illustrate use cases of the toolbox and demos/reproduce_journal_results contains scripts that replicate the evaluations from our paper.

The plugin supports most of the commonly used file types such as HDF5, tiff stacks and matlab mat files. To run the motion compensation, the options need to be defined into a OF_options object such as

options = OF_options(...
    'input_file', 'input.hdf', ... % input path
    'output_path', results_folder, ... % results folder
    'output_format', 'MAT', ...
    'alpha', [0.5, 0.5], ... % smoothness parameter
    'sigma', [0.5, 0.5, 0.1; ... % gauss kernel size channel 1
              0.5, 0.5, 0.1], ... % gauss kernel size channel 2
    'weight', [1, 1], ...
    'levels', 15, ... % solver levels
    'eta', 0.86, ... % pyramid stepsize
    'iterations', 25, ... % outer iterations (the larger the better the result, but slower)
    'bin_size', 5, ... % binning over 5 frames from the 30 hz data
    'buffer_size', 500, ... % size of blocks for the parallel evaluation (larger takes more memory)
    'output_typename', [], ...
    'reference_frames', 1:5 ...
    );

The object is then passed to compensate_recording(options) to run the motion compensation on input.hdf into results_folder. To run compensate_recording with default parameters, only the input file and output path need to be specified.

Dataset

The dataset which we used for our evaluations is available as 2-Photon Movies with Motion Artifacts.

Citation

Details on the method and video results can be found here.

If you use parts of this code or the plugin for your work, please cite

P. Flotho, S. Nomura, B. Kuhn and D. J. Strauss, “Software for Non-Parametric Image Registration of 2-Photon Imaging Data,” J Biophotonics, 2022. doi:https://doi.org/10.1002/jbio.202100330

BibTeX entry

@article{flotea2022a,
    author = {Flotho, P. and Nomura, S. and Kuhn, B. and Strauss, D. J.},
    title = {Software for Non-Parametric Image Registration of 2-Photon Imaging Data},
    year = {2022},
  journal = {J Biophotonics},
  doi = {https://doi.org/10.1002/jbio.202100330}
}