{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:19:16Z","timestamp":1792790356555,"version":"4.5.0"},"reference-count":72,"publisher":"eLife Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:00:00Z","timestamp":1790294400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:00:00Z","timestamp":1790294400000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:00:00Z","timestamp":1790294400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Institut national de recherche en sciences et technologies du num\u00e9rique","award":["ANR-24-RRII-000"],"award-info":[{"award-number":["ANR-24-RRII-000"]}],"id":[{"id":"https:\/\/ror.org\/02kvxyf05","id-type":"ROR","asserted-by":"crossref"}]},{"award":["ANR-24-RRII-000"],"award-info":[{"award-number":["ANR-24-RRII-000"]}],"id":[{"id":"https:\/\/ror.org\/02kvxyf05","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Agence Nationale de la Recherche","award":["ANR-25-CE42-6535-03"],"award-info":[{"award-number":["ANR-25-CE42-6535-03"]}],"id":[{"id":"https:\/\/ror.org\/00rbzpz17","id-type":"ROR","asserted-by":"crossref"}]},{"award":["ANR-25-CE42-6535-03"],"award-info":[{"award-number":["ANR-25-CE42-6535-03"]}],"id":[{"id":"https:\/\/ror.org\/00rbzpz17","id-type":"ROR","asserted-by":"publisher"}]},{"name":"National Institutes of Health","award":["T32GM144273"],"award-info":[{"award-number":["T32GM144273"]}]},{"award":["T32GM144273"],"award-info":[{"award-number":["T32GM144273"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Biotechnology and Biological Sciences Research Council","award":["BB\/X01861X\/1"],"award-info":[{"award-number":["BB\/X01861X\/1"]}],"id":[{"id":"https:\/\/ror.org\/00cwqg982","id-type":"ROR","asserted-by":"crossref"}]},{"award":["BB\/X01861X\/1"],"award-info":[{"award-number":["BB\/X01861X\/1"]}],"id":[{"id":"https:\/\/ror.org\/00cwqg982","id-type":"ROR","asserted-by":"publisher"}]},{"name":"National Science Foundation","award":["DBI-1707398"],"award-info":[{"award-number":["DBI-1707398"]}]},{"award":["DBI-1707398"],"award-info":[{"award-number":["DBI-1707398"]}],"id":[{"id":"https:\/\/ror.org\/021nxhr62","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Simons Foundation","award":["344 543023"],"award-info":[{"award-number":["344 543023"]}],"id":[{"id":"https:\/\/ror.org\/01cmst727","id-type":"ROR","asserted-by":"crossref"}]},{"award":["344 543023"],"award-info":[{"award-number":["344 543023"]}],"id":[{"id":"https:\/\/ror.org\/01cmst727","id-type":"ROR","asserted-by":"publisher"}]},{"name":"National Institutes of Health","award":["U19NS123716-02"],"award-info":[{"award-number":["U19NS123716-02"]}]},{"award":["U19NS123716-02"],"award-info":[{"award-number":["U19NS123716-02"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"name":"National Institutes of Health","award":["T32GM007753"],"award-info":[{"award-number":["T32GM007753"]}]},{"award":["T32GM007753"],"award-info":[{"award-number":["T32GM007753"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"name":"National Institutes of Health","award":["F31129103"],"award-info":[{"award-number":["F31129103"]}]},{"award":["F31129103"],"award-info":[{"award-number":["F31129103"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":["elifesciences.org"],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>Spike sorting is an algorithmic process that extracts the activity of individual neurons from extracellular electrophysiology recordings. With the ballooning use of high-density probes, such as Neuropixels, this essential processing step is increasingly becoming time-consuming and computationally expensive. Although many software tools have been proposed to address spike sorting, they are usually constructed and benchmarked as monolithic \u2018black boxes\u2019, making it difficult to factor out the effects of individual algorithmic steps on the final outcome, especially when varying datasets and parameters. To address this issue, we developed a modular and common framework to develop, benchmark, and assemble the key computational steps that are used in state-of-the-art spike sorting algorithms. Relying on fast and efficient ground truth generation of biophysically plausible recordings, we show that we are able to individually benchmark and precisely quantify the performance of different steps in a spike sorting pipeline (i.e. peak detection, feature extraction, clustering, and template matching). We then leverage these results to create a modular, component-based spike sorter that can outperform Kilosort4 on dense and large simulated recordings, and produce similar quantitative results on real data. In addition, we find that the major bottleneck of all modern spike sorting pipelines is in the physical motion of probes, regardless of the drift-correction strategy. The component-based spike sorting framework presented here has the potential to foster community engagement in the field by lowering the barrier to contributions and providing a flexible yet powerful framework to construct end-to-end spike sorting solutions.<\/jats:p>","DOI":"10.7554\/elife.110588","type":"journal-article","created":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T16:30:17Z","timestamp":1775061017000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.110588","source":"Crossref","is-referenced-by-count":0,"title":["Opening the black box toward a modular approach to spike sorting"],"prefix":"10.7554","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6389-9779","authenticated-orcid":true,"given":"Samuel","family":"Garcia","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00pdd0432","id-type":"ROR","asserted-by":"publisher"}],"name":"Centre de Recherche en Neuroscience de Lyon, CNRS","place":["Lyon, France"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Chris","family":"Halcrow","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01nrxwf90","id-type":"ROR","asserted-by":"publisher"}],"name":"University of Edinburgh","place":["Edinburgh, United Kingdom"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Charlie","family":"Windolf","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00hj8s172","id-type":"ROR","asserted-by":"publisher"}],"name":"Columbia University","place":["New York, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"}]},{"given":"Zachary M","family":"McKenzie","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03vek6s52","id-type":"ROR","asserted-by":"publisher"}],"name":"Harvard Medical School","place":["Boston, United States"]},{"id":[{"id":"https:\/\/ror.org\/002pd6e78","id-type":"ROR","asserted-by":"publisher"}],"name":"Massachusetts General Hospital","place":["Boston, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Paul","family":"Adkisson-Floro","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01d74sk53","id-type":"ROR","asserted-by":"publisher"}],"name":"CatalystNeuro","place":["Casper, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"}]},{"given":"Heberto Ramon","family":"Mayorquin","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01d74sk53","id-type":"ROR","asserted-by":"publisher"}],"name":"CatalystNeuro","place":["Casper, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"}]},{"given":"Benjamin K","family":"Dichter","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01d74sk53","id-type":"ROR","asserted-by":"publisher"}],"name":"CatalystNeuro","place":["Casper, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"methodology","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3661-527X","authenticated-orcid":true,"given":"Alessio Paolo","family":"Buccino","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01d74sk53","id-type":"ROR","asserted-by":"publisher"}],"name":"CatalystNeuro","place":["Casper, United States"]},{"id":[{"id":"https:\/\/ror.org\/04szwah67","id-type":"ROR","asserted-by":"publisher"}],"name":"Allen Institute for Neural Dynamics","place":["Seattle, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1376-5240","authenticated-orcid":true,"given":"Pierre","family":"Yger","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04p94ax69","id-type":"ROR","asserted-by":"publisher"}],"name":"Lille Neurosciences & Cognition (LilNCog) \u2013 U1172 (INSERM, Lille), Univ Lille","place":["Lille, France"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"4374","published-online":{"date-parts":[[2026,9,25]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1016\/j.bios.2018.10.032","type":"journal-article","article-title":"SiNAPS: An implantable active pixel sensor CMOS-probe for simultaneous large-scale neural recordings","volume":"126","author":"Angotzi","year":"2019","journal-title":"Biosensors & Bioelectronics"},{"key":"bib2","doi-asserted-by":"publisher","DOI":"10.1002\/advs.202416239","type":"journal-article","article-title":"Multi-Shank 1024 channels active SiNAPS probe for large multi-regional topographical electrophysiological mapping of neural dynamics","volume":"12","author":"Angotzi","year":"2025","journal-title":"Advanced Science"},{"key":"bib3","doi-asserted-by":"publisher","DOI":"10.48324\/dandi.000409\/0.260309.1324","type":"software","article-title":"IBL - brain wide map","volume-title":"DANDI Archive","author":"Benson","year":"2026","unstructured":"Benson J, Birman D, Bonacchi N, Carandini M, Catarino J, Chapuis G, Dayan P, DeWitt E, Engel T, Fabbri M, Faulkner M, Fiete I, Findling C, Freitas-Silva L, Ger\u00e7ek B, Harris K, Hofer S, Hu F, Hubert F, Huntenburg J, Khanal A, Langdon C, Lau P, Meijer G, Miska N, Noel JP, Nylund K, Pan-Vazquez A, Pouget A, Rossant C, Roth N, Schaeffer R, Schartner M, Shi Y, Socha K, Steinmetz N, Svoboda K, Urai A, Wells M, West S, Whiteway M, Winter O, Witten I, International Brain Laboratory. 2026. IBL - brain wide map. DANDI Archive. 0.260309.1324. https:\/\/doi.org\/10.48324\/dandi.000409\/0.260309.1324."},{"key":"bib4","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1109\/IPEC51340.2021.9421295","type":"conference-paper","article-title":"Overview of match pursuit algorithms and application comparison in image reconstruction","author":"Bian","year":"2021","unstructured":"Bian S, Zhang L. 2021. Overview of match pursuit algorithms and application comparison in image reconstruction. 2021 IEEE Asia-Pacific Conference on Image Processing, Electronics and Computers (IPEC)."},{"key":"bib5","doi-asserted-by":"publisher","DOI":"10.1088\/1742-5468\/2008\/10\/P10008","type":"journal-article","article-title":"Fast unfolding of communities in large networks","volume":"2008","author":"Blondel","year":"2008","journal-title":"Journal of Statistical Mechanics"},{"key":"bib6","doi-asserted-by":"publisher","DOI":"10.1101\/2023.08.11.553023","type":"preprint","article-title":"DARTsort: A modular drift tracking spike sorter for high-density multi-electrode probes","volume-title":"bioRxiv","author":"Boussard","year":"2023"},{"key":"bib7","doi-asserted-by":"publisher","DOI":"10.1101\/691642","type":"preprint","article-title":"MEArec: A fast and customizable testbench simulator for ground-truth extracellular spiking activity","volume-title":"bioRxiv","author":"Buccino","year":"2020"},{"key":"bib8","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.61834","type":"journal-article","article-title":"SpikeInterface, a unified framework for spike sorting","volume":"9","author":"Buccino","year":"2020","journal-title":"eLife"},{"key":"bib9","doi-asserted-by":"publisher","DOI":"10.1088\/2516-1091\/ac6b96","type":"journal-article","article-title":"Spike sorting: new trends and challenges of the era of high-density probes","volume":"4","author":"Buccino","year":"2022","journal-title":"Progress in Biomedical Engineering"},{"key":"bib10","type":"software","article-title":"Spikeinterface","volume-title":"Software Heritage","author":"Buccino","year":"2026","unstructured":"Buccino A, Halcrow C, Mayorquin H, McKenzie Z. 2026a. Spikeinterface. Software Heritage. swh:1:rev:b17c60f8f620f40cc224a805e4a639f799b93980. https:\/\/archive.softwareheritage.org\/swh:1:dir:a0a34dadb01c24545f159f0ba2eae9ad0e24fc1c;origin=https:\/\/github.com\/SpikeInterface\/spikeinterface;visit=swh:1:snp:00505c2e4d6baa3332c0ae02d2d637149a97a3bc;anchor=swh:1:rev:b17c60f8f620f40cc224a805e4a639f799b93980."},{"key":"bib11","doi-asserted-by":"publisher","DOI":"10.1101\/2025.11.12.687966","type":"preprint","article-title":"Efficient and reproducible pipelines for spike sorting large-scale electrophysiology data","volume-title":"bioRxiv","author":"Buccino","year":"2026"},{"key":"bib12","doi-asserted-by":"publisher","first-page":"1859","DOI":"10.1152\/jn.00339.2018","type":"journal-article","article-title":"A novel and fully automatic spike-sorting implementation with variable number of features","volume":"120","author":"Chaure","year":"2018","journal-title":"Journal of Neurophysiology"},{"key":"bib13","doi-asserted-by":"publisher","first-page":"1381","DOI":"10.1016\/j.neuron.2017.08.030","type":"journal-article","article-title":"A fully automated approach to spike sorting","volume":"95","author":"Chung","year":"2017","journal-title":"Neuron"},{"key":"bib14","doi-asserted-by":"publisher","first-page":"3155","DOI":"10.1152\/jn.00803.2017","type":"journal-article","article-title":"Automatic spike sorting for high-density microelectrode arrays","volume":"120","author":"Diggelmann","year":"2018","journal-title":"Journal of Neurophysiology"},{"key":"bib15","doi-asserted-by":"publisher","first-page":"782","DOI":"10.1038\/s41593-024-01588-5","type":"journal-article","article-title":"Local origin of excitatory\u2013inhibitory tuning equivalence in a cortical network","volume":"27","author":"Duszkiewicz","year":"2024","journal-title":"Nature Neuroscience"},{"key":"bib16","type":"dataset","article-title":"Large-scale recordings of head direction cells in mouse postsubiculum","volume-title":"DANDI","author":"Duszkiewicz","year":"2025","unstructured":"Duszkiewicz A, Carrasco SS, Peyrache A. 2025. Large-scale recordings of head direction cells in mouse postsubiculum. DANDI. https:\/\/dandiarchive.org\/dandiset\/000939\/0.250207.0025."},{"key":"bib17","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/j.neunet.2020.11.009","type":"journal-article","article-title":"Deep-learned spike representations and sorting via an ensemble of auto-encoders","volume":"134","author":"Eom","year":"2021","journal-title":"Neural Networks"},{"key":"bib18","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.8172822","type":"software","article-title":"Bombcell: automated curation and cell classification of spike-sorted electrophysiology data","volume-title":"Zenodo","author":"Fabre","year":"2023","unstructured":"Fabre JMJ, Peters AJ, Carandini M, Harris KD. 2023. Bombcell: automated curation and cell classification of spike-sorted electrophysiology data. Zenodo. 1.0.0. https:\/\/doi.org\/10.5281\/zenodo.8172822."},{"key":"bib19","doi-asserted-by":"publisher","DOI":"10.3389\/fninf.2022.823056","type":"journal-article","article-title":"ProbeInterface: A unified framework for probe handling in extracellular electrophysiology","volume":"16","author":"Garcia","year":"2022","journal-title":"Frontiers in Neuroinformatics"},{"key":"bib20","doi-asserted-by":"publisher","DOI":"10.1523\/ENEURO.0105-22.2022","type":"journal-article","article-title":"How do spike collisions affect spike sorting performance?","volume":"9","author":"Garcia","year":"2022","journal-title":"eNeuro"},{"key":"bib21","doi-asserted-by":"publisher","DOI":"10.1523\/ENEURO.0229-23.2023","type":"journal-article","article-title":"A modular implementation to handle and benchmark drift correction for high-density extracellular recordings","volume":"11","author":"Garcia","year":"2024","journal-title":"eNeuro"},{"key":"bib22","doi-asserted-by":"publisher","DOI":"10.1088\/1741-2552\/ae0d33","type":"journal-article","article-title":"E-Sort: empowering end-to-end neural network for multi-channel spike sorting with transfer learning and fast post-processing","volume":"22","author":"Han","year":"2025","journal-title":"Journal of Neural Engineering"},{"key":"bib23","doi-asserted-by":"publisher","DOI":"10.1101\/2024.10.14.618046","type":"preprint","article-title":"End-to-end multimodal deep learning for real-time decoding of months-long neural activity from the same cells","volume-title":"bioRxiv","author":"He","year":"2024"},{"key":"bib24","doi-asserted-by":"publisher","first-page":"2521","DOI":"10.1016\/j.celrep.2017.02.038","type":"journal-article","article-title":"Unsupervised spike sorting for large-scale, high-density multielectrode arrays","volume":"18","author":"Hilgen","year":"2017","journal-title":"Cell Reports"},{"key":"bib25","doi-asserted-by":"publisher","DOI":"10.1038\/s41378-025-01046-7","type":"journal-article","article-title":"Microelectrode arrays cultured with in vitro neural networks for motion control tasks: encoding and decoding progress and advances","volume":"11","author":"Hua","year":"2025","journal-title":"Microsystems & Nanoengineering"},{"key":"bib26","doi-asserted-by":"publisher","DOI":"10.1101\/2025.03.30.645770","type":"preprint","article-title":"UnitRefine: A community toolbox for automated spike sorting curation","volume-title":"bioRxiv","author":"Jain","year":"2025"},{"key":"bib27","doi-asserted-by":"publisher","DOI":"10.1101\/101030","type":"preprint","article-title":"Real-time spike sorting platform for high-density extracellular probes with ground-truth validation and drift correction","volume-title":"bioRxiv","author":"Jun","year":"2017"},{"key":"bib28","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1038\/nature24636","type":"journal-article","article-title":"Fully integrated silicon probes for high-density recording of neural activity","volume":"551","author":"Jun","year":"2017","journal-title":"Nature"},{"key":"bib29","doi-asserted-by":"publisher","DOI":"10.1088\/1741-2552\/aa6089","type":"journal-article","article-title":"Noise-robust unsupervised spike sorting based on discriminative subspace learning with outlier handling","volume":"14","author":"Keshtkaran","year":"2017","journal-title":"Journal of Neural Engineering"},{"key":"bib30","doi-asserted-by":"publisher","DOI":"10.1101\/2025.06.20.660590","type":"preprint","article-title":"SLAy-Ing oversplitting errors in high-density electrophysiology spike sorting","volume-title":"bioRxiv","author":"Koukuntla","year":"2025"},{"key":"bib31","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-48456-y","type":"journal-article","article-title":"A normalized template matching method for improving spike detection in extracellular voltage recordings","volume":"9","author":"Laboy-Ju\u00e1rez","year":"2019","journal-title":"Scientific Reports"},{"key":"bib32","doi-asserted-by":"publisher","DOI":"10.1101\/2024.12.04.626805","type":"preprint","article-title":"Spike sorting biases and information loss in a detailed cortical model","volume-title":"bioRxiv","author":"Laquitaine","year":"2024"},{"key":"bib33","doi-asserted-by":"publisher","DOI":"10.5522\/04\/24411841","type":"dataset","article-title":"Chronic recordings from Neuropixels 2.0 probes in mice","volume-title":"Figshare","author":"Lebedeva","year":"2023","unstructured":"Lebedeva A, Okun M, Krumins MK, Carandini M. 2023. Chronic recordings from Neuropixels 2.0 probes in mice. Figshare. https:\/\/doi.org\/10.5522\/04\/24411841."},{"key":"bib34","doi-asserted-by":"publisher","DOI":"10.1101\/2020.03.18.997924","type":"preprint","article-title":"YASS: Yet another spike sorter applied to large-scale multi-electrode array recordings in primate retina","volume-title":"bioRxiv","author":"Lee","year":"2020"},{"key":"bib35","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/j.jphysparis.2017.02.005","type":"journal-article","article-title":"Recent progress in multi-electrode spike sorting methods","volume":"110","author":"Lefebvre","year":"2016","journal-title":"Journal of Physiology, Paris"},{"key":"bib36","type":"preprint","article-title":"Efficient batched CPU\/GPU implementation of orthogonal matching pursuit for python","volume-title":"arXiv","author":"Lubonja","year":"2024","unstructured":"Lubonja A, Pr\u00e6sius SK, Tran TD. 2024. Efficient batched CPU\/GPU implementation of orthogonal matching pursuit for python. arXiv. https:\/\/arxiv.org\/html\/2407.06434v1."},{"key":"bib37","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.1508.04841","type":"preprint","article-title":"Unimodal clustering using isotonic regression: ISO-SPLIT","volume-title":"arXiv","author":"Magland","year":"2016"},{"key":"bib38","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.55167","type":"journal-article","article-title":"SpikeForest, reproducible web-facing ground-truth validation of automated neural spike sorters","volume":"9","author":"Magland","year":"2020","journal-title":"eLife"},{"key":"bib39","doi-asserted-by":"publisher","first-page":"3397","DOI":"10.1109\/78.258082","type":"journal-article","article-title":"Matching pursuits with time-frequency dictionaries","volume":"41","author":"Mallat","year":"1993","journal-title":"IEEE Transactions on Signal Processing"},{"key":"bib40","doi-asserted-by":"publisher","DOI":"10.21105\/joss.00205","type":"journal-article","article-title":"hdbscan: Hierarchical density based clustering","volume":"2","author":"McInnes","year":"2017","journal-title":"The Journal of Open Source Software"},{"key":"bib41","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1038\/s41559-023-02008-w","type":"journal-article","article-title":"Better incentives are needed to reward academic software development","volume":"7","author":"Merow","year":"2023","journal-title":"Nature Ecology & Evolution"},{"key":"bib42","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1038\/s41586-025-09235-0","type":"journal-article","article-title":"A brain-wide map of neural activity during complex behaviour","volume":"645","author":"Meshulam","year":"2025","journal-title":"Nature"},{"key":"bib43","first-page":"4448","type":"conference-paper","article-title":"Fast and accurate spike sorting of high-channel count probes with kilosort","author":"Pachitariu","year":"2016","unstructured":"Pachitariu M, Steinmetz NA, Kadir SN. 2016. Fast and accurate spike sorting of high-channel count probes with kilosort. Advances in Neural Information Processing Systems."},{"key":"bib44","type":"software","article-title":"Kilosort2","volume-title":"Github","author":"Pachitariu","year":"2019","unstructured":"Pachitariu M, Steinmetz NA, Colonell J. 2019. Kilosort2. Github. 17743f2. https:\/\/github.com\/MouseLand\/Kilosort2."},{"key":"bib45","doi-asserted-by":"publisher","DOI":"10.1101\/2023.01.07.523036","type":"preprint","article-title":"Solving the spike sorting problem with kilosort","volume-title":"bioRxiv","author":"Pachitariu","year":"2023"},{"key":"bib46","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1038\/s41592-024-02232-7","type":"journal-article","article-title":"Spike sorting with Kilosort4","volume":"21","author":"Pachitariu","year":"2024","journal-title":"Nature Methods"},{"key":"bib47","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1109\/ACSSC.1993.342465","type":"conference-paper","article-title":"Orthogonal matching pursuit: recursive function approximation with applications to wavelet decomposition","author":"Pati","year":"1993","unstructured":"Pati YC, Rezaiifar R, Krishnaprasad PS. 1993. Orthogonal matching pursuit: recursive function approximation with applications to wavelet decomposition. 27th Asilomar Conference on Signals, Systems and Computers."},{"key":"bib48","doi-asserted-by":"publisher","first-page":"1661","DOI":"10.1162\/089976604774201631","type":"journal-article","article-title":"Unsupervised spike detection and sorting with wavelets and superparamagnetic clustering","volume":"16","author":"Quiroga","year":"2004","journal-title":"Neural Computation"},{"key":"bib49","doi-asserted-by":"publisher","first-page":"634","DOI":"10.1038\/nn.4268","type":"journal-article","article-title":"Spike sorting for large, dense electrode arrays","volume":"19","author":"Rossant","year":"2016","journal-title":"Nature Neuroscience"},{"key":"bib50","doi-asserted-by":"publisher","DOI":"10.3390\/electronics10040410","type":"journal-article","article-title":"Comparison of sneo-based neural spike detection algorithms for implantable multi-transistor array biosensors","volume":"10","author":"Saggese","year":"2021","journal-title":"Electronics"},{"key":"bib51","type":"software","article-title":"Sorting_components_benchmark_paper","volume-title":"Software Heritage","author":"Samuel","year":"2026","unstructured":"Samuel G, Halcrow C. 2026. Sorting_components_benchmark_paper. Software Heritage. swh:1:rev:d93ca4e101c822dfe12b99cc59bdb9d0ca1045b1. https:\/\/archive.softwareheritage.org\/swh:1:dir:8cfbafcc54daf55b3c40fc48305997c724132827;origin=https:\/\/github.com\/SpikeInterface\/sorting_components_benchmark_paper;visit=swh:1:snp:a05ae97de8e6ac34e7d31a6732afbed6b5b1ff98;anchor=swh:1:rev:d93ca4e101c822dfe12b99cc59bdb9d0ca1045b1."},{"key":"bib52","doi-asserted-by":"publisher","first-page":"4844","DOI":"10.1039\/d5lc00058k","type":"journal-article","article-title":"Advances in large-scale electrophysiology with high-density microelectrode arrays","volume":"25","author":"Schr\u00f6ter","year":"2025","journal-title":"Lab on a Chip"},{"key":"bib53","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1109\/BioCAS49922.2021.9644995","type":"conference-paper","article-title":"A modulated template-matching approach to improve spike sorting of bursting neurons","author":"Shabestari","year":"2021","unstructured":"Shabestari PS, Buccino AP, Kumar SS, Pedrocchi A, Hierlemann A. 2021. A modulated template-matching approach to improve spike sorting of bursting neurons. IEEE Biomedical Circuits and Systems Conference."},{"key":"bib54","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-39986-6","type":"journal-article","article-title":"Spike sorting with Gaussian mixture models","volume":"9","author":"Souza","year":"2019","journal-title":"Scientific Reports"},{"key":"bib55","doi-asserted-by":"publisher","DOI":"10.6084\/m9.figshare.14024495","type":"dataset","article-title":"\u201cImposed motion datasets\u201d from Steinmetz et al. Science 2021","volume-title":"Figshare","author":"Steinmetz","year":"2021","unstructured":"Steinmetz N. 2021. \u201cImposed motion datasets\u201d from Steinmetz et al. Science 2021. Figshare. https:\/\/doi.org\/10.6084\/m9.figshare.14024495."},{"key":"bib56","doi-asserted-by":"publisher","DOI":"10.1126\/science.abf4588","type":"journal-article","article-title":"Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings","volume":"372","author":"Steinmetz","year":"2021","journal-title":"Science"},{"key":"bib57","doi-asserted-by":"publisher","DOI":"10.1016\/j.jneumeth.2023.110017","type":"journal-article","article-title":"Simulation of background neuronal activity and noise in human intracranial microwire recordings","volume":"402","author":"Steinmetz","year":"2024","journal-title":"Journal of Neuroscience Methods"},{"key":"bib58","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-93088-w","type":"journal-article","article-title":"An automatic spike sorting algorithm based on adaptive spike detection and a mixture of skew-t distributions","volume":"11","author":"Toosi","year":"2021","journal-title":"Scientific Reports"},{"key":"bib59","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1109\/TIT.1960.1057571","type":"journal-article","article-title":"An introduction to matched filters","volume":"6","author":"Turin","year":"1960","journal-title":"IEEE Transactions on Information Theory"},{"key":"bib60","doi-asserted-by":"publisher","DOI":"10.1109\/ICASSP39728.2021.9414145","type":"conference-paper","article-title":"Decentralized motion inference and registration of neuropixel data","author":"Varol","year":"2021","unstructured":"Varol E, Boussard J, Dethe N, Winter O, Urai A, Brain Laboratory TI, Churchland A, Steinmetz N, Paninski L. 2021. Decentralized motion inference and registration of neuropixel data. ICASSP 2021 - 2021 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)."},{"key":"bib61","doi-asserted-by":"publisher","DOI":"10.1101\/2024.11.06.622160","type":"preprint","article-title":"MEDiCINe: Motion correction for neural electrophysiology recordings","volume-title":"bioRxiv","author":"Watters","year":"2024"},{"key":"bib62","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1038\/s41592-025-02614-5","type":"journal-article","article-title":"DREDge: robust motion correction for high-density extracellular recordings across species","volume":"22","author":"Windolf","year":"2025","journal-title":"Nature Methods"},{"key":"bib63","doi-asserted-by":"publisher","DOI":"10.1016\/j.xpro.2025.104195","type":"journal-article","article-title":"Protocol for the enhanced analysis of electrophysiological data from high-density multi-electrode arrays with nicespike and spikeNburst","volume":"6","author":"Wolff","year":"2025","journal-title":"STAR Protocols"},{"key":"bib64","doi-asserted-by":"publisher","DOI":"10.1088\/1741-2552\/aace8a","type":"journal-article","article-title":"Towards online spike sorting for high-density neural probes using discriminative template matching with suppression of interfering spikes","volume":"15","author":"Wouters","year":"2018","journal-title":"Journal of Neural Engineering"},{"key":"bib65","doi-asserted-by":"publisher","first-page":"4376","DOI":"10.1109\/EMBC.2019.8856930","type":"conference-paper","article-title":"A data-driven regularization approach for template matching in spike sorting with high-density neural probes","author":"Wouters","year":"2019","unstructured":"Wouters J, Kloosterman F, Bertrand A. 2019. A data-driven regularization approach for template matching in spike sorting with high-density neural probes. 2019 41st Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)."},{"key":"bib66","doi-asserted-by":"publisher","DOI":"10.1088\/1741-2552\/ac0f4a","type":"journal-article","article-title":"A data-driven spike sorting feature map for resolving spike overlap in the feature space","volume":"18","author":"Wouters","year":"2021","journal-title":"Journal of Neural Engineering"},{"key":"bib67","doi-asserted-by":"publisher","DOI":"10.1101\/2022.02.08.479192","type":"preprint","article-title":"Lussac: A fully-automated consensus method that increases the yield and quality of spike-sorting analyses","volume-title":"bioRxiv","author":"Wyngaard","year":"2022"},{"key":"bib68","doi-asserted-by":"publisher","first-page":"3966","DOI":"10.1016\/j.neuron.2025.08.030","type":"journal-article","article-title":"Ultra-high-density Neuropixels probes improve detection and identification in neuronal recordings","volume":"113","author":"Ye","year":"2025","journal-title":"Neuron"},{"key":"bib69","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.34518","type":"journal-article","article-title":"A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo","volume":"7","author":"Yger","year":"2018","journal-title":"eLife"},{"key":"bib70","type":"software","article-title":"Spikeinterface-kilosort-components","volume-title":"Softwre Heritage","author":"Yger","year":"2026","unstructured":"Yger P, Samuel G, Buccino A. 2026. Spikeinterface-kilosort-components. Softwre Heritage. swh:1:rev:0b5bb63e3055e3f751ef36890acb60feea7160e1. https:\/\/archive.softwareheritage.org\/swh:1:dir:307c9734a2622cc20cc35f926679a9caabdc1a09;origin=https:\/\/github.com\/SpikeInterface\/spikeinterface-kilosort-components;visit=swh:1:snp:3981a714cb6c6dcc8d8006fe7c11354b24a0ea1f;anchor=swh:1:rev:0b5bb63e3055e3f751ef36890acb60feea7160e1."},{"key":"bib71","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-19771-8","type":"journal-article","article-title":"A robust spike sorting method based on the joint optimization of linear discrimination analysis and density peaks","volume":"12","author":"Zhang","year":"2022","journal-title":"Scientific Reports"},{"key":"dataset1","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.20407862","type":"dataset","article-title":"Script and notebook for the paper \"Opening the black box: a modular approach to spike sorting\"","volume-title":"Zenodo","author":"Garcia","year":"2026","unstructured":"Garcia S, Yger P, Buccino A, Halcrow C. 2026. Script and notebook for the paper \"Opening the black box: a modular approach to spike sorting\". Zenodo."}],"container-title":["eLife"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdn.elifesciences.org\/articles\/110588\/elife-110588-v1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdn.elifesciences.org\/articles\/110588\/elife-110588-v1.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/elifesciences.org\/articles\/110588","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T15:45:48Z","timestamp":1790351148000},"score":1,"resource":{"primary":{"URL":"https:\/\/elifesciences.org\/articles\/110588"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,25]]},"references-count":72,"alternative-id":["10.7554\/eLife.110588"],"URL":"https:\/\/doi.org\/10.7554\/elife.110588","archive":["CLOCKSS"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.64898\/2026.01.23.701239","asserted-by":"subject"}],"references":[{"id-type":"uri","id":"https:\/\/dandiarchive.org\/dandiset\/000939\/0.250207.0025","asserted-by":"subject"},{"id-type":"doi","id":"10.5522\/04\/24411841","asserted-by":"subject"},{"id-type":"doi","id":"10.6084\/m9.figshare.14024495","asserted-by":"subject"}],"is-same-as":[{"id-type":"doi","id":"10.7554\/eLife.110588.3","asserted-by":"subject"}],"is-version-of":[{"id-type":"doi","id":"10.7554\/eLife.110588.1","asserted-by":"subject"},{"id-type":"doi","id":"10.7554\/eLife.110588.2","asserted-by":"subject"}],"is-supplemented-by":[{"id-type":"doi","id":"10.5281\/zenodo.20407862","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/archive.softwareheritage.org\/swh:1:dir:a0a34dadb01c24545f159f0ba2eae9ad0e24fc1c;origin=https:\/\/github.com\/SpikeInterface\/spikeinterface;visit=swh:1:snp:00505c2e4d6baa3332c0ae02d2d637149a97a3bc;anchor=swh:1:rev:b17c60f8f620f40cc224a805e4a639f799b93980","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/archive.softwareheritage.org\/swh:1:dir:8cfbafcc54daf55b3c40fc48305997c724132827;origin=https:\/\/github.com\/SpikeInterface\/sorting_components_benchmark_paper;visit=swh:1:snp:a05ae97de8e6ac34e7d31a6732afbed6b5b1ff98;anchor=swh:1:rev:d93ca4e101c822dfe12b99cc59bdb9d0ca1045b1","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/archive.softwareheritage.org\/swh:1:dir:307c9734a2622cc20cc35f926679a9caabdc1a09;origin=https:\/\/github.com\/SpikeInterface\/spikeinterface-kilosort-components;visit=swh:1:snp:3981a714cb6c6dcc8d8006fe7c11354b24a0ea1f;anchor=swh:1:rev:0b5bb63e3055e3f751ef36890acb60feea7160e1","asserted-by":"subject"}]},"ISSN":["2050-084X"],"issn-type":[{"value":"2050-084X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,25]]},"assertion":[{"value":"single anonymised","name":"peer_review_transparency","label":"Peer review transparency","group":{"name":"peer_review_taxonomy"}},{"value":"other reviewer(s), editor","name":"peer_review_interaction","label":"Peer review interaction","group":{"name":"peer_review_taxonomy"}},{"value":"review summaries, review reports, author\/editor communication, reviewer identities reviewer opt in, editor identities","name":"peer_review_published","label":"Peer review published","group":{"name":"peer_review_taxonomy"}},{"value":"open (sign in with ORCID iD required)","name":"post_publication_commenting","label":"Post publication commenting","group":{"name":"post_publication_commenting"}}],"article-number":"RP110588"}}