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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 foundhere and the project website with video resultshere.

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

Pleasecontact us for more details.

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

This repository contains the demo scriptsdemos/jupiter.m anddemos/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 folderdemos/examples contains examples that illustrate use cases of the toolbox anddemos/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 aOF_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 tocompensate_recording(options) to run the motion compensation oninput.hdf intoresults_folder. To runcompensate_recording with default parameters, only the input file and output path need to be specified.

The dataset which we used for our evaluations is available as2-Photon Movies with Motion Artifacts.

Details on the method and video results can be foundhere.

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}}