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Toolbox for fast, variational 1D alignment

The code is written in Matlab and C++. The preprint of our paper can be found on bioRxiv and the project website here.

Download

Download the repository via

$ git clone https://github.com/phflot/variational_aligner.git

ImageJ and Fiji Plugin

An ImageJ and Fiji plugin for the alignment of linescans is available here.

Documentation and Usage

The Code can be compiled and installed with the set_path.m file. The file examples/align_noise.m reproduces the alignment of random data from our paper and can be referred to for the usage of the alignment functions. The script examples/linescan_example.m demonstrates the alignment of 2D multichannel linescan data.

Citation

If you use this code for your work, please cite

Flotho, P., Thinnes, D., Kuhn, B., Roome, C. J., Vibell, J. F., & Strauss, D. J. (2021). Fast variational alignment of non-flat 1D displacements for applications in neuroimaging. Journal of Neuroscience Methods, 353, 109076.

BibTeX entry

@article{floth21,
  title={Fast variational alignment of non-flat 1D displacements for applications in neuroimaging},
  author={Flotho, Philipp and Thinnes, David and Kuhn, Bernd and Roome, Christopher J and Vibell, Jonas F and Strauss, Daniel J},
  journal = {Journal of Neuroscience Methods},
  volume = {353},
  pages = {109076},
  year = {2021},
  issn = {0165-0270},
  doi = {https://doi.org/10.1016/j.jneumeth.2021.109076},
  url = {https://www.sciencedirect.com/science/article/pii/S016502702100011X},
}

If you use this work in the context of EP and ERP analysis, please additionally cite

D. Thinnes, P. Flotho, F. I. Corona-Strauss, D. J. Strauss and J. F. Vibell, “Compensation of P300 Latency Jitter using fast variational 1D Displacement Estimation” (in preparation), 2020.

BibTeX entry

@article{thinn20,
    author = {Thinnes, D. and Flotho, P. and Corona-Strauss, F. I. and Strauss, D. J. and Vibell, J. F.},
    title = {Compensation of P300 Latency Jitter using fast variational 1D Displacement Estimation},
    journal = {(in preparation)},
    year = {2020}
}