{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T17:40:47Z","timestamp":1781199647170,"version":"3.54.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008806","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,4,26]],"date-time":"2021-04-26T00:00:00Z","timestamp":1619395200000}}],"reference-count":38,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2021,4,14]],"date-time":"2021-04-14T00:00:00Z","timestamp":1618358400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000997","name":"Arnold and Mabel Beckman Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000997","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000997","name":"Arnold and Mabel Beckman Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100000997","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100001201","name":"Kavli Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001201","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001201","name":"Kavli Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001201","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Voltage imaging enables monitoring neural activity at sub-millisecond and sub-cellular scale, unlocking the study of subthreshold activity, synchrony, and network dynamics with unprecedented spatio-temporal resolution. However, high data rates (&gt;800MB\/s) and low signal-to-noise ratios create bottlenecks for analyzing such datasets. Here we present\n                    <jats:italic>VolPy<\/jats:italic>\n                    , an automated and scalable pipeline to pre-process voltage imaging datasets.\n                    <jats:italic>VolPy<\/jats:italic>\n                    features motion correction, memory mapping, automated segmentation, denoising and spike extraction, all built on a highly parallelizable, modular, and extensible framework optimized for memory and speed. To aid automated segmentation, we introduce a corpus of 24 manually annotated datasets from different preparations, brain areas and voltage indicators. We benchmark\n                    <jats:italic>VolPy<\/jats:italic>\n                    against ground truth segmentation, simulations and electrophysiology recordings, and we compare its performance with existing algorithms in detecting spikes. Our results indicate that\n                    <jats:italic>VolPy<\/jats:italic>\n                    \u2019s performance in spike extraction and scalability are state-of-the-art.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1008806","type":"journal-article","created":{"date-parts":[[2021,4,14]],"date-time":"2021-04-14T19:04:19Z","timestamp":1618427059000},"page":"e1008806","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":48,"title":["VolPy: Automated and scalable analysis pipelines for voltage imaging datasets"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1091-5365","authenticated-orcid":true,"given":"Changjia","family":"Cai","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1321-5866","authenticated-orcid":true,"given":"Johannes","family":"Friedrich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6413-2040","authenticated-orcid":true,"given":"Amrita","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3934-1609","authenticated-orcid":true,"given":"M. Hossein","family":"Eybposh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1509-6394","authenticated-orcid":true,"given":"Eftychios A.","family":"Pnevmatikakis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0374-2005","authenticated-orcid":true,"given":"Kaspar","family":"Podgorski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7850-444X","authenticated-orcid":true,"given":"Andrea","family":"Giovannucci","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,4,14]]},"reference":[{"issue":"6","key":"pcbi.1008806.ref001","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1016\/j.cell.2016.11.021","article-title":"Cell-type specific optical recording of membrane voltage dynamics in freely moving mice","volume":"167","author":"JD Marshall","year":"2016","journal-title":"Cell"},{"issue":"1","key":"pcbi.1008806.ref002","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1523\/JNEUROSCI.0594-14.2015","article-title":"Imaging the Awake Visual Cortex with a Genetically Encoded Voltage Indicator","volume":"35","author":"M Carandini","year":"2015","journal-title":"Journal of Neuroscience"},{"issue":"8","key":"pcbi.1008806.ref003","doi-asserted-by":"crossref","first-page":"2323","DOI":"10.1152\/jn.00452.2012","article-title":"Imaging neural circuit dynamics with a voltage-sensitive fluorescent protein","volume":"108","author":"W Akemann","year":"2012","journal-title":"Journal of Neurophysiology"},{"key":"pcbi.1008806.ref004","first-page":"1","article-title":"Optical voltage imaging in neurons: moving from technology development to practical tool","author":"T Kn\u00f6pfel","year":"2019","journal-title":"Nature Reviews Neuroscience"},{"issue":"6454","key":"pcbi.1008806.ref005","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1126\/science.aav6416","article-title":"Bright and photostable chemigenetic indicators for extended in vivo voltage imaging","volume":"365","author":"AS Abdelfattah","year":"2019","journal-title":"Science"},{"issue":"7756","key":"pcbi.1008806.ref006","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/s41586-019-1166-7","article-title":"Voltage imaging and optogenetics reveal behaviour-dependent changes in hippocampal dynamics","volume":"569","author":"Y Adam","year":"2019","journal-title":"Nature"},{"issue":"12","key":"pcbi.1008806.ref007","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1038\/s41592-018-0188-7","article-title":"Fast, in vivo voltage imaging using a red fluorescent indicator","volume":"15","author":"M Kannan","year":"2018","journal-title":"Nature methods"},{"key":"pcbi.1008806.ref008","first-page":"616094","article-title":"Population imaging of neural activity in awake behaving mice in multiple brain regions","author":"KD Piatkevich","year":"2019","journal-title":"bioRxiv"},{"issue":"4","key":"pcbi.1008806.ref009","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1038\/s41589-018-0004-9","article-title":"A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters","volume":"14","author":"KD Piatkevich","year":"2018","journal-title":"Nature chemical biology"},{"issue":"1","key":"pcbi.1008806.ref010","doi-asserted-by":"crossref","first-page":"3388","DOI":"10.1038\/s41467-018-05900-3","article-title":"Simultaneous dendritic voltage and calcium imaging and somatic recording from Purkinje neurons in awake mice","volume":"9","author":"CJ Roome","year":"2018","journal-title":"Nature communications"},{"key":"pcbi.1008806.ref011","doi-asserted-by":"crossref","unstructured":"Buchanan EK, Kinsella I, Zhou D, Zhu R, Zhou P, Gerhard F, et al. 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