automatic-spike-detection 1.3.0

Python library for automatically detecting interictal epileptiform discharges (IEDs) by means of nonnegative matrix factorization (NMF)

automatic-spike-detection

The automatic-spike-detection package is a Python library for automatically detecting interictal epileptiform discharges (IEDs) in intracranial EEG (iEEG) recordings.

IEDs, also referred to as ”spikes”, are a characteristic of the epileptic brain that are recognizable as large transient events in the electroencephalogram of patients living with epilepsy [1]. Whereas, for clinicians, IEDs can provide valuable information about the epileptogenic zone, for researchers, they can also be a source of noise and need to be excluded, such as in [2] where Cusinato and Alnes et al. studied how the human brain processes sounds. Regardless of the context, the localization of IEDs in EEG recordings is a very time-consuming task.

This package aims to contribute to this issue by building on an algorithm previously developed by Baud et al. [3] that employs nonnegative matrix factorization (NMF) to automatically detect IEDs, an unsupervised machine-learning algorithm that produces a lower-dimensional approximation of the input.

It is important to note, that the algorithm used by this package is optimized for and was solely tested on iEEG recordings. Intracranial EEG is an invasive technique with implanted electrodes that is used for clinical monitoring, e.g. to identify the epileptogenic zone and prepare for epilepsy surgery. The primary characteristic of iEEG is that it provides high spatial and temporal resolution of the electrical activity in the brain, which makes it a valuable resource for neuroscientific research as well [4].

Please consult the automatic-spike-detection Documentation for details on the underlying concepts of the algorithm, the Installation and Usage , and the application programming interface (API)

Contributions

In addition to the dependencies in the requirements.txt file, you need to install the dependencies listed in the dev-requirements.txt file, which provides some formatting tools:

pip install requirements.txt
pip install dev-requirements.txt

References

[1] Marco de Curtis and Giuliano Avanzini. "Interictal spikes in focal epileptogenesis". Progress in Neurobiology 63, no.5 (2001): 541-567.

[2] Riccardo Cusinato, Sigurd L. Alnes, Ellen van Maren, Ida Boccalaro, Debora Ledergerber, Antoine Adamantidis, Lukas L. Imbach, Kaspar Schindler, Maxime O. Baud, and Athina Tzovara. Intrinsic neural timescales in the temporal lobe support an auditory processing hierarchy. Journal of Neuroscience, 43(20):3696–3707, 2023.

[3] Maxime O. Baud, Jonathan K. Kleen, Gopala K. Anumanchipalli, Liberty S. Hamilton, Yee-Leng Tan, Robert Knowlton, and Edward F. Chang. Unsupervised learning of spatiotemporal interictal discharges in focal epilepsy. Neurosurgery, 83(4), 2018.

[4] Elizabeth L Johnson, Julia W Y Kam, Athina Tzovara, and Robert T Knight. Insights into human cognition from intracranial eeg: A review of audition, memory, internal cognition, and causality. Journal of Neural Engineering, 17(5):051001, oct 2020.