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 [Garcia2024] as well as the references that correspond to the preset you used:

nonrigid_accurate [Windolf_a] [Varol]
nonrigid_fast_and_accurate [Windolf_a] [Varol] [Pachitariu]
rigid_fast no additional citation needed
kilosort_like [Pachitariu]
dredge_ap [Windolf_b]
dredge_lfp [Windolf_b]
medicine [Watters]

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]
rtsort [van_der_Molen]
spykingcircus [Yger]
wavclus [Chaure]
yass [Lee]

Postprocessing Module

If you use the postprocessing module, i.e. you use the analyzer.compute() include the citations for the following methods:

acgs_3d [Beau]

unit_locations or spike_locations with monopolar_triangulation based on work from [Boussard]

unit_locations or spike_locations with grid_convolution based on work from [Pachitariu]

template_metrics [Jia]

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]

If you use auto_label_units or train_model, please cite [Jain]

Benchmark

For addicts to benchmarking numerical methods in the context of spike sorting, if you use the benchmark module please cite [Garcia2022], [Garcia2024] or [Scopin2024].