Separating gamma oscillations from broadband activity to understand stimulus specificity of gamma oscillations (Hermes, Miller, Wandell and Winawer, 2015, Cerebral Cortex doi: 10.1093/cercor/bhu091)

• Matlab code: https://github.com/dorahermes/Paper_Hermes_2015_CerCortex
• Data: https://academic.oup.com/cercor/article/25/9/2951/2926112#supplementary-data

An image-computable model for the stimulus selectivity of gamma oscillations (Hermes, Petridou, Kay, Winawer, 2019 eLife 8:e47035 https://doi.org/10.7554/eLife.47035 )

• Matlab code: https://github.com/dorahermes/Paper_Hermes_2019_eLife
• Data: https://osf.io/q4yad/  

Basis profile curve identification clusters different ECoG responses in a single electrode after stimulating may other electrodes with a single pulse (Miller, Mueller & Hermes, PLoS Comp Biol, 2021: https://doi.org/10.1371/journal.pcbi.1008710)

• Data and Matlab code: https://purl.stanford.edu/rc201dv0636
• Data in BIDS: https://openneuro.org/datasets/ds003708
• Python code: https://github.com/MultimodalNeuroimagingLab/bpc_jupyter

Jon Kleen: "Avoid sharp edges and always check your references"

Spike detection - line-length based detector providing onset/offset time stamps and index of involved channels for epileptiform spikes in multichannel time series data (spike detection artifact, detection, and suggested guidelines: Ammanuel*, Kleen* et al., Frontiers in Human Neuroscience, 2020) https://doi.org/10.3389/fnhum.2020.00044)

• Matlab: https://github.com/Kleen-Lab/Linelength-spike-detector-MATLAB
• Python: https://github.com/Kleen-Lab/Linelength-spike-detector-PYTHON

Ictal Cinema / OPSCEA (Omni-planar and surface casting of epileoptiform activity) - Generate movies of intracranial-EEG seizure activity projected as a heatmap on a patient's own reconstructed brain surfaces (Kleen et al, Epilepsia, 2021: https://doi.org/10.1111/epi.16841)

• Matlab code: https://github.com/Kleen-Lab/OPSCEA
• Sample data to make practice videos: https://osf.io/49znp

Andrea Navas-Olive​: "HFO detection and feature extraction with convolutional neural networks"

Sharp-wave ripple detector using CNNs

• Code for Python: https://github.com/PridaLab/cnn-ripple
• Code for Matlab: https://github.com/PridaLab/cnn-matlab

Open Ephys custom plugin - for closed loop detection and intervention (soon available in their web):

• https://github.com/PridaLab/CNNRippleDetectorOEPlugin

Channel-interpolation Open Ephys plugin - for probes that are not ultradense this allows interpolating existing channels to add more density, improving CNN performance:

• https://github.com/PridaLab/ChInterpolationOEPlugin

Helpful Overview Papers and Packages for Neuroscience/Electrophysiology Methodology and Best Practices

• Recommendations for the Design and Analysis of In Vivo Electrophysiology Studies (Journal of Neuroscience 27 June 2018, 38 (26) 5837-5839; DOI: https://doi.org/10.1523/JNEUROSCI.1480-18.2018)
• The origin of extracellular fields and currents — EEG, ECoG, LFP and spikes (Nat Rev Neurosci 13, 407–420 (2012). https://doi.org/10.1038/nrn3241)

Other Helpful Packages for Neuroscience/Electrophysiology Methodology

• Framework for analyzing single cells (https://cellexplorer.org)