How to Cite

If you like SpikeInterface, please star us on Github! giving us a star gives a measure of the level of use and interest, which goes a long way to getting funding

Please cite SpikeInterface in your papers with our eLife paper: [Buccino]

SpikeInterface stands on the shoulders of giants! Each method in SpikeInterface draws on (or directly runs) independently-created methods. Please try to reference the individual works that are important for your analysis pipeline. If you notice a missing reference, please let us know by submitting an issue on Github.

Preprocessing Module

If you use one of the following preprocessing methods, please cite the appropriate source:

phase_shift or highpass_spatial_filter [IBL]
detect_bad_channels(method='coherence+psd') [IBL]
common_reference [Rolston]

Motion Correction

If you use the correct_motion method in the preprocessing module, please cite [Garcia] as well as the references that correspond to the preset you used:

nonrigid_accurate [Windolf] [Varol]
nonrigid_fast_and_accurate [Windolf] [Varol] [Pachitariu]
rigid_fast no additional citation needed
kilosort_like [Pachitariu]

Sorters Module

If you use one of the following spike sorting algorithms (i.e. you use the run_sorter() method, please include the appropriate citation for the sorter_name parameter you use: Note: unless otherwise stated, the reference given is to be used for all versions of the sorter

combinato [Niediek]
hdsort [Diggelmann]
herdingspikes [Muthmann] [Hilgen]
kilosort [Pachitariu]
mountainsort [Chung]
spykingcircus [Yger]
wavclus [Chaure]
yass [Lee]

Qualitymetrics Module

If you use the qualitymetrics module, i.e. you use the analyzer.compute() or compute_quality_metrics() methods, please include the citations for the metric_names that were particularly important for your research:

amplitude_cutoff [Hill]
amplitude_median [IBL]
sliding_rp_violation [IBL]
drift [Siegle]
isi_violation [UMS]
rp_violation [Llobet]
sd_ratio [Pouzat]
snr [Lemon] [Jackson]
synchrony [Grün]

If you use the qualitymetrics.pca_metrics module, i.e. you use the compute_pc_metrics() method, please include the citations for the metric_names that were particularly important for your research:

d_prime [Hill]
isolation_distance or l_ratio [Schmitzer-Torbert]
nearest_neighbor or nn_isolation or nn_noise_overlap [Chung] [Siegle]
silhouette [Rousseeuw] [Hruschka]

Curation Module

If you use the get_potential_auto_merge method from the curation module, please cite [Llobet]

References

SpikeInterface, a unified framework for spike sorting. 2020.

[Buzsáki]

The Log-Dynamic Brain: How Skewed Distributions Affect Network Operations. 2014.

A novel and fully automatic spike-sorting implementation with variable number of features. 2018.

[Chung]

(1, 2) A Fully Automated Approach to Spike Sorting. 2017.

Automatic spike sorting for high-density microelectrode arrays. 2018.

A Modular Implementation to Handle and Benchmark Drift Correction for High-Density Extracellular Recordings. 2024.

Impact of higher-order correlations on coincidence distributions of massively parallel data. 2007.

[Harris]

Temporal interaction between single spikes and complex spike bursts in hippocampal pyramidal cells. 2001.

Unsupervised Spike Sorting for Large-Scale, High-Density Multielectrode Arrays. 2017.

[Hill]

(1, 2) Quality Metrics to Accompany Spike Sorting of Extracellular Signals. 2011.

Evolutionary algorithms for clustering gene-expression data. 2004.

[IBL]

(1, 2, 3, 4) Spike sorting pipeline for the International Brain Laboratory. 2022.

Quantitative assessment of extracellular multichannel recording quality using measures of cluster separation. Society of Neuroscience Abstract. 2005.

YASS: Yet another spike sorter. 2017.

Methods for neuronal recording in conscious animals. IBRO Handbook Series. 1984.

[Llobet]

(1, 2) Automatic post-processing and merging of multiple spike-sorting analyses with Lussac. 2022.

Spike Detection for Large Neural Populations Using High Density Multielectrode Arrays. 2015.

Reliable Analysis of Single-Unit Recordings from the Human Brain under Noisy Conditions: Tracking Neurons over Hours. 2016.

[Pachitariu]

(1, 2, 3) Spike sorting with Kilosort4. 2024.

Using noise signature to optimize spike-sorting and to assess neuronal classification quality. 2002.

Common median referencing for improved action potential detection with multielectrode arrays. 2009.

Silhouettes: A graphical aid to the interpretation and validation of cluster analysis. 1987.

[Schmitzer-Torbert]

Neuronal Activity in the Rodent Dorsal Striatum in Sequential Navigation: Separation of Spatial and Reward Responses on the Multiple T Task. 2004.

[Siegle]

(1, 2) Survey of Spiking in the Mouse Visual System Reveals Functional Hierarchy. 2021.

UltraMegaSort2000 - Spike sorting and quality metrics for extracellular spike data. 2011.

[Varol]

(1, 2) Decentralized Motion Inference and Registration of Neuropixel Data. 2021.

[Windolf]

(1, 2) Robust Online Multiband Drift Estimation in Electrophysiology Data. 2022.

A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo. 2018.