Automatic objective neuronal spike detection

Automatic objective neuronal spike detection for electrophys. measurements. ALPHA VERSION.

ALPHA VERSION!

Especially the handeling of signals not confirming to our model has not been fully implemented.

Also some of the user selectable parameters have not yet been implemented.

Bugs exists.

FENS 2022 poster: https://homepages.tuni.fi/jarno.tanskanen/conferences/FENS2022/Tanskanen-FENS2022-A0.pdf

Please, submit possible suggestions, and enrol to a mailing list to be informed of new versions by email to jarno.tanskanen(at)tuni.fi.

Please, visit again. Thank you!

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New version upcoming by the Forum of European Neuroscience (9.-13.7.2022)!

The function is complete but not exhaustively tested. Comments may also be incomplete.

Also checking the histogram gradient's properties is insufficient for general use, i.e., histograms with no usable features are not screened for; this has been planned for a future version. Currently, the user must observe the gradient images to check that the gradient possesed features resulting in useful thresholds.

Citing

When describing any use or modification of the program or the method, whether in its original or derivative form, please, cite [1]. The method originally proposed in [2] and a version of the function was also presented at [3], which may optionally be sited in addition to [1].

References

[1] J. M. A. Tanskanen, F. E. Kapucu, I. Vornanen, and J. A. K. Hyttinen, "Automatic objective thresholding to detect neuronal action potentials," in Proc. 24th European Signal Processing Conference (EUSIPCO 2016), Budapest, Hungary, Aug.-Sept. 2016, pp. 662–666. https://doi.org/10.1109/EUSIPCO.2016.7760331

[2] J. M. A. Tanskanen, F. E. Kapucu, and J. A. K. Hyttinen, "On the threshold based neuronal spike detection, and an objective criterion for setting the threshold," in Proc. 7th Annual International IEEE EMBS Conference on Neural Engineering (NER'15), Montpellier, France, Apr. 2015, pp. 1016–1019. http://dx.doi.org/10.1109/NER.2015.7146799

[3] J. M. A. Tanskanen, F. E. Kapucu, I. Vornanen, K. Lenk, and J. Hyttinen, "Objective thresholding of MEA data for action potential detection, " Front. Neurosci. Conference Abstract: MEA Meeting 2016 | 10th International Meeting on Substrate-Integrated Electrode Arrays. http://dx.doi.org/10.3389/conf.fnins.2016.93.00028