{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:13:21Z","timestamp":1772172801776,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008330","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,12,10]],"date-time":"2020-12-10T00:00:00Z","timestamp":1607558400000}}],"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2020,11,30]],"date-time":"2020-11-30T00:00:00Z","timestamp":1606694400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"crossref","award":["DP170102263"],"award-info":[{"award-number":["DP170102263"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"crossref","award":["DP180100636"],"award-info":[{"award-number":["DP180100636"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>The pattern of neural activity evoked by a stimulus can be substantially affected by ongoing spontaneous activity. Separating these two types of activity is particularly important for calcium imaging data given the slow temporal dynamics of calcium indicators. Here we present a statistical model that decouples stimulus-driven activity from low dimensional spontaneous activity in this case. The model identifies hidden factors giving rise to spontaneous activity while jointly estimating stimulus tuning properties that account for the confounding effects that these factors introduce. By applying our model to data from zebrafish optic tectum and mouse visual cortex, we obtain quantitative measurements of the extent that neurons in each case are driven by evoked activity, spontaneous activity, and their interaction. By not averaging away potentially important information encoded in spontaneous activity, this broadly applicable model brings new insight into population-level neural activity within single trials.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008330","type":"journal-article","created":{"date-parts":[[2020,11,30]],"date-time":"2020-11-30T14:28:56Z","timestamp":1606746536000},"page":"e1008330","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":23,"title":["Model-based decoupling of evoked and spontaneous neural activity in calcium imaging data"],"prefix":"10.1371","volume":"16","author":[{"given":"Marcus A.","family":"Triplett","sequence":"first","affiliation":[]},{"given":"Zac","family":"Pujic","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3896-7861","authenticated-orcid":true,"given":"Biao","family":"Sun","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1957-8702","authenticated-orcid":true,"given":"Lilach","family":"Avitan","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9789-9355","authenticated-orcid":true,"given":"Geoffrey J.","family":"Goodhill","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,11,30]]},"reference":[{"issue":"5283","key":"pcbi.1008330.ref001","doi-asserted-by":"crossref","first-page":"1868","DOI":"10.1126\/science.273.5283.1868","article-title":"Dynamics of ongoing activity: explanation of the large variability in evoked cortical responses","volume":"273","author":"A Arieli","year":"1996","journal-title":"Science"},{"issue":"6437","key":"pcbi.1008330.ref002","doi-asserted-by":"crossref","DOI":"10.1126\/science.aav7893","article-title":"Spontaneous behaviors drive multidimensional, brainwide activity","volume":"364","author":"C Stringer","year":"2019","journal-title":"Science"},{"key":"pcbi.1008330.ref003","first-page":"308288","article-title":"Single-trial neural dynamics are dominated by richly varied movements","author":"S Musall","year":"2019","journal-title":"bioRxiv"},{"issue":"7419","key":"pcbi.1008330.ref004","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1038\/nature11529","article-title":"Retinal waves coordinate patterned activity throughout the developing visual system","volume":"490","author":"JB Ackman","year":"2012","journal-title":"Nature"},{"issue":"6437","key":"pcbi.1008330.ref005","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1126\/science.aav3932","article-title":"Thirst regulates motivated behavior through modulation of brainwide neural population dynamics","volume":"364","author":"WE Allen","year":"2019","journal-title":"Science"},{"issue":"7458","key":"pcbi.1008330.ref006","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1038\/nature12354","article-title":"Ultrasensitive fluorescent proteins for imaging neuronal activity","volume":"499","author":"TW Chen","year":"2013","journal-title":"Nature"},{"issue":"2","key":"pcbi.1008330.ref007","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1016\/j.bpj.2008.08.005","article-title":"Spike inference from calcium imaging using sequential Monte Carlo methods","volume":"97","author":"JT Vogelstein","year":"2009","journal-title":"Biophysical Journal"},{"key":"pcbi.1008330.ref008","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1016\/j.conb.2018.04.007","article-title":"Neural data science: accelerating the experiment-analysis-theory cycle in large-scale neuroscience","volume":"50","author":"L Paninski","year":"2018","journal-title":"Current Opinion in Neurobiology"},{"key":"pcbi.1008330.ref009","unstructured":"Byron MY, Cunningham JP, Santhanam G, Ryu SI, Shenoy KV, Sahani M. 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