Citation guide

Mesmerize provides interfaces to many great tools that were created by other developers. I encourage citing the tools that you use in addition to citing Mesmerize.

Mesmerize relies heavily on pyqtgraph widgets. Citing pyqtgraph.

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Module Cite
CNMF
Giovannucci A., Friedrich J., Gunn P., Kalfon J., Brown, B., Koay S.A., Taxidis J., Najafi F., Gauthier J.L., Zhou P., Baljit, K.S., Tank D.W., Chklovskii D.B., Pnevmatikakis E.A. (2019). CaImAn: An open source tool for scalable Calcium Imaging data Analysis. eLife 8, e38173. https://elifesciences.org/articles/38173
Pnevmatikakis, E.A., Soudry, D., Gao, Y., Machado, T., Merel, J., … & Paninski, L. (2016). Simultaneous denoising, deconvolution, and demixing of calcium imaging data. Neuron 89(2):285-299. http://dx.doi.org/10.1016/j.neuron.2015.11.037
Pnevmatikakis, E.A., Gao, Y., Soudry, D., Pfau, D., Lacefield, C., … & Paninski, L. (2014). A structured matrix factorization framework for large scale calcium imaging data analysis. arXiv preprint arXiv:1409.2903. http://arxiv.org/abs/1409.2903
CNMFE
In addition to the above CNMF papers:
Zhou, P., Resendez, S. L., Rodriguez-Romaguera, J., Jimenez, J. C., Neufeld, S. Q., Giovannucci, A., … Paninski, L. (2018). Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data. ELife, 7. doi: https://doi.org/10.7554/eLife.28728.001
Caiman Motion Correction
Giovannucci A., Friedrich J., Gunn P., Kalfon J., Brown, B., Koay S.A., Taxidis J., Najafi F., Gauthier J.L., Zhou P., Baljit, K.S., Tank D.W., Chklovskii D.B., Pnevmatikakis E.A. (2019). CaImAn: An open source tool for scalable Calcium Imaging data Analysis. eLife 8, e38173. https://elifesciences.org/articles/38173
Pnevmatikakis, E.A., and Giovannucci A. (2017). NoRMCorre: An online algorithm for piecewise rigid motion correction of calcium imaging data. Journal of Neuroscience Methods, 291:83-92. https://doi.org/10.1016/j.jneumeth.2017.07.031

Nodes/Analysis

Node/Method Cite
k-Shape clustering
Paparrizos, J., & Gravano, L. (2016). k-Shape. ACM SIGMOD Record, 45(1), 69–76. doi: http://dx.doi.org/10.1145/2723372.2737793
Tavenard, R., Faouzi, J., & Vandewiele, G.. (2017). tslearn: A machine learning toolkit dedicated to time-series data. https://github.com/rtavenar/tslearn
Cross-correlation
Tavenard, R., Faouzi, J., & Vandewiele, G.. (2017). tslearn: A machine learning toolkit dedicated to time-series data. https://github.com/rtavenar/tslearn
TVDiff Node Rick Chartrand, “Numerical Differentiation of Noisy, Nonsmooth Data,” ISRN Applied Mathematics, vol. 2011, Article ID 164564, 11 pages, 2011. https://doi.org/10.5402/2011/164564.