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: - :code:`phase_shift` or :code:`highpass_spatial_filter` [IBL]_ - :code:`detect_bad_channels(method='coherence+psd')` [IBL]_ - :code:`common_reference` [Rolston]_ Motion Correction ^^^^^^^^^^^^^^^^^ If you use the :code:`correct_motion` method in the preprocessing module, please cite [Garcia]_ as well as the references that correspond to the :code:`preset` you used: - :code:`nonrigid_accurate` [Windolf]_ [Varol]_ - :code:`nonrigid_fast_and_accurate` [Windolf]_ [Varol]_ [Pachitariu]_ - :code:`rigid_fast` *no additional citation needed* - :code:`kilosort_like` [Pachitariu]_ Sorters Module -------------- If you use one of the following spike sorting algorithms (i.e. you use the :code:`run_sorter()` method, please include the appropriate citation for the :code:`sorter_name` parameter you use: *Note: unless otherwise stated, the reference given is to be used for all versions of the sorter* - :code:`combinato` [Niediek]_ - :code:`hdsort` [Diggelmann]_ - :code:`herdingspikes` [Muthmann]_ [Hilgen]_ - :code:`kilosort` [Pachitariu]_ - :code:`mountainsort` [Chung]_ - :code:`spykingcircus` [Yger]_ - :code:`wavclus` [Chaure]_ - :code:`yass` [Lee]_ Qualitymetrics Module --------------------- If you use the :code:`qualitymetrics` module, i.e. you use the :code:`analyzer.compute()` or :code:`compute_quality_metrics()` methods, please include the citations for the :code:`metric_names` that were particularly important for your research: - :code:`amplitude_cutoff` [Hill]_ - :code:`amplitude_median` [IBL]_ - :code:`sliding_rp_violation` [IBL]_ - :code:`drift` [Siegle]_ - :code:`isi_violation` [UMS]_ - :code:`rp_violation` [Llobet]_ - :code:`sd_ratio` [Pouzat]_ - :code:`snr` [Lemon]_ [Jackson]_ - :code:`synchrony` [Grün]_ If you use the :code:`qualitymetrics.pca_metrics` module, i.e. you use the :code:`compute_pc_metrics()` method, please include the citations for the :code:`metric_names` that were particularly important for your research: - :code:`d_prime` [Hill]_ - :code:`isolation_distance` or :code:`l_ratio` [Schmitzer-Torbert]_ - :code:`nearest_neighbor` or :code:`nn_isolation` or :code:`nn_noise_overlap` [Chung]_ [Siegle]_ - :code:`silhouette` [Rousseeuw]_ [Hruschka]_ Curation Module --------------- If you use the :code:`get_potential_auto_merge` method from the curation module, please cite [Llobet]_ References ---------- .. [Buccino] `SpikeInterface, a unified framework for spike sorting. 2020. `_ .. [Buzsáki] `The Log-Dynamic Brain: How Skewed Distributions Affect Network Operations. 2014. `_ .. [Chaure] `A novel and fully automatic spike-sorting implementation with variable number of features. 2018. `_ .. [Chung] `A Fully Automated Approach to Spike Sorting. 2017. `_ .. [Diggelmann] `Automatic spike sorting for high-density microelectrode arrays. 2018. `_ .. [Garcia] `A Modular Implementation to Handle and Benchmark Drift Correction for High-Density Extracellular Recordings. 2024. `_ .. [Grün] `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. `_ .. [Hilgen] `Unsupervised Spike Sorting for Large-Scale, High-Density Multielectrode Arrays. 2017. `_ .. [Hill] `Quality Metrics to Accompany Spike Sorting of Extracellular Signals. 2011. `_ .. [Hruschka] `Evolutionary algorithms for clustering gene-expression data. 2004. `_ .. [IBL] `Spike sorting pipeline for the International Brain Laboratory. 2022. `_ .. [Jackson] Quantitative assessment of extracellular multichannel recording quality using measures of cluster separation. Society of Neuroscience Abstract. 2005. .. [Lee] `YASS: Yet another spike sorter. 2017. `_ .. [Lemon] Methods for neuronal recording in conscious animals. IBRO Handbook Series. 1984. .. [Llobet] `Automatic post-processing and merging of multiple spike-sorting analyses with Lussac. 2022. `_ .. [Muthmann] `Spike Detection for Large Neural Populations Using High Density Multielectrode Arrays. 2015. `_ .. [Niediek] `Reliable Analysis of Single-Unit Recordings from the Human Brain under Noisy Conditions: Tracking Neurons over Hours. 2016. `_ .. [Pachitariu] `Spike sorting with Kilosort4. 2024. `_ .. [Pouzat] `Using noise signature to optimize spike-sorting and to assess neuronal classification quality. 2002. `_ .. [Rolston] `Common median referencing for improved action potential detection with multielectrode arrays. 2009. `_ .. [Rousseeuw] `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] `Survey of Spiking in the Mouse Visual System Reveals Functional Hierarchy. 2021. `_ .. [UMS] `UltraMegaSort2000 - Spike sorting and quality metrics for extracellular spike data. 2011. `_ .. [Varol] `Decentralized Motion Inference and Registration of Neuropixel Data. 2021. `_ .. [Windolf] `Robust Online Multiband Drift Estimation in Electrophysiology Data. 2022. `_ .. [Yger] `A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo. 2018. `_