{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T21:47:41Z","timestamp":1793224061439,"version":"4.5.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008256","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,3,18]],"date-time":"2021-03-18T00:00:00Z","timestamp":1616025600000}}],"reference-count":24,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2021,3,8]],"date-time":"2021-03-08T00:00:00Z","timestamp":1615161600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5RO1NS073129"],"award-info":[{"award-number":["5RO1NS073129"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5RO1DA036913"],"award-info":[{"award-number":["5RO1DA036913"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["RF1MH114132"],"award-info":[{"award-number":["RF1MH114132"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U19MH114821"],"award-info":[{"award-number":["U19MH114821"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01MH109113"],"award-info":[{"award-number":["U01MH109113"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1U19NS107613"],"award-info":[{"award-number":["1U19NS107613"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000882","name":"Brain Research Foundation","doi-asserted-by":"crossref","award":["BRF-SIA-2014-03"],"award-info":[{"award-number":["BRF-SIA-2014-03"]}],"id":[{"id":"10.13039\/100000882","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100011039","name":"Intelligence Advanced Research Projects Activity","doi-asserted-by":"crossref","award":["D16PC0008"],"award-info":[{"award-number":["D16PC0008"]}],"id":[{"id":"10.13039\/100011039","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100011039","name":"Intelligence Advanced Research Projects Activity","doi-asserted-by":"publisher","award":["D16PC0003"],"award-info":[{"award-number":["D16PC0003"]}],"id":[{"id":"10.13039\/100011039","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Paul Allen Distinguished Investigator Award"},{"DOI":"10.13039\/100000893","name":"Simons Foundation","doi-asserted-by":"publisher","award":["350789"],"award-info":[{"award-number":["350789"]}],"id":[{"id":"10.13039\/100000893","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014989","name":"Chan Zuckerberg Initiative","doi-asserted-by":"crossref","award":["2017-0530"],"award-info":[{"award-number":["2017-0530"]}],"id":[{"id":"10.13039\/100014989","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100014989","name":"Chan Zuckerberg Initiative","doi-asserted-by":"crossref","award":["2018-183188"],"award-info":[{"award-number":["2018-183188"]}],"id":[{"id":"10.13039\/100014989","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Robert Lourie"},{"name":"Assistant Secretary of Defense for Health Affairs","award":["W81XWH1910083"],"award-info":[{"award-number":["W81XWH1910083"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Modern spatial transcriptomics methods can target thousands of different types of RNA transcripts in a single slice of tissue. Many biological applications demand a high spatial density of transcripts relative to the imaging resolution, leading to partial mixing of transcript rolonies in many voxels; unfortunately, current analysis methods do not perform robustly in this highly-mixed setting. Here we develop a new analysis approach,\n                    <jats:italic>BARcode DEmixing through Non-negative Spatial Regression<\/jats:italic>\n                    (BarDensr): we start with a generative model of the physical process that leads to the observed image data and then apply sparse convex optimization methods to estimate the underlying (demixed) rolony densities. We apply BarDensr to simulated and real data and find that it achieves state of the art signal recovery, particularly in densely-labeled regions or data with low spatial resolution. Finally, BarDensr is fast and parallelizable. We provide open-source code as well as an implementation for the \u2018NeuroCAAS\u2019 cloud platform.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1008256","type":"journal-article","created":{"date-parts":[[2021,3,8]],"date-time":"2021-03-08T13:41:38Z","timestamp":1615210898000},"page":"e1008256","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":29,"title":["BARcode DEmixing through Non-negative Spatial Regression (BarDensr)"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2673-3558","authenticated-orcid":true,"given":"Shuonan","family":"Chen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4751-8910","authenticated-orcid":true,"given":"Jackson","family":"Loper","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2807-6125","authenticated-orcid":true,"given":"Xiaoyin","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex","family":"Vaughan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony M.","family":"Zador","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liam","family":"Paninski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,3,8]]},"reference":[{"issue":"9","key":"pcbi.1008256.ref001","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1038\/nmeth.2563","article-title":"In situ sequencing for RNA analysis in preserved tissue and cells","volume":"10","author":"R Ke","year":"2013","journal-title":"Nature methods"},{"issue":"4","key":"pcbi.1008256.ref002","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1038\/nmeth.2892","article-title":"Single-cell in situ RNA profiling by sequential hybridization","volume":"11","author":"E Lubeck","year":"2014","journal-title":"Nature methods"},{"issue":"6233","key":"pcbi.1008256.ref003","doi-asserted-by":"crossref","first-page":"aaa6090","DOI":"10.1126\/science.aaa6090","article-title":"Spatially resolved, highly multiplexed RNA profiling in single cells","volume":"348","author":"KH Chen","year":"2015","journal-title":"Science"},{"key":"pcbi.1008256.ref004","article-title":"Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems","author":"S Alon","year":"2020","journal-title":"bioRxiv"},{"issue":"1","key":"pcbi.1008256.ref005","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/s41592-019-0631-4","article-title":"Probabilistic cell typing enables fine mapping of closely related cell types in situ","volume":"17","author":"X Qian","year":"2020","journal-title":"Nature methods"},{"issue":"39","key":"pcbi.1008256.ref006","doi-asserted-by":"crossref","first-page":"11046","DOI":"10.1073\/pnas.1612826113","article-title":"High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization","volume":"113","author":"JR Moffitt","year":"2016","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"2","key":"pcbi.1008256.ref007","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1016\/j.neuron.2016.10.001","article-title":"In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus","volume":"92","author":"S Shah","year":"2016","journal-title":"Neuron"},{"issue":"6400","key":"pcbi.1008256.ref008","doi-asserted-by":"crossref","first-page":"eaat5691","DOI":"10.1126\/science.aat5691","article-title":"Three-dimensional intact-tissue sequencing of single-cell transcriptional states","volume":"361","author":"X Wang","year":"2018","journal-title":"Science"},{"key":"pcbi.1008256.ref009","article-title":"Hybridization-based In Situ Sequencing (HybISS): spatial transcriptomic detection in human and mouse brain tissue","author":"D Gyllborg","year":"2020","journal-title":"bioRxiv"},{"issue":"6177","key":"pcbi.1008256.ref010","doi-asserted-by":"crossref","first-page":"1360","DOI":"10.1126\/science.1250212","article-title":"Highly multiplexed subcellular RNA sequencing in situ","volume":"343","author":"JH Lee","year":"2014","journal-title":"Science"},{"issue":"6416","key":"pcbi.1008256.ref011","doi-asserted-by":"crossref","first-page":"eaau5324","DOI":"10.1126\/science.aau5324","article-title":"Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region","volume":"362","author":"JR Moffitt","year":"2018","journal-title":"Science"},{"key":"pcbi.1008256.ref012","article-title":"Neuroscience Cloud Analysis As a Service","author":"T Abe","year":"2020","journal-title":"bioRxiv"},{"issue":"3","key":"pcbi.1008256.ref013","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1016\/j.cell.2019.09.023","article-title":"High-throughput mapping of long-range neuronal projection using in situ sequencing","volume":"179","author":"X Chen","year":"2019","journal-title":"Cell"},{"key":"pcbi.1008256.ref014","article-title":"Integrating barcoded neuroanatomy with spatial transcriptional profiling reveals cadherin correlates of projections shared across the cortex","author":"YC Sun","year":"2020","journal-title":"bioRxiv"},{"issue":"2","key":"pcbi.1008256.ref015","doi-asserted-by":"crossref","DOI":"10.14440\/jbm.2014.36","article-title":"Advanced methods of microscope control using \u03bcManager software","volume":"1","author":"AD Edelstein","year":"2014","journal-title":"Journal of biological methods"},{"key":"pcbi.1008256.ref016","volume-title":"Chapman & Hall\/CRC Monographs on Statistics & Applied Probability","author":"T Hastie","year":"2015"},{"key":"pcbi.1008256.ref017","unstructured":"Nogueira F. Bayesian Optimization: Open source constrained global optimization tool for Python; 2014. Available from: https:\/\/github.com\/fmfn\/BayesianOptimization."},{"key":"pcbi.1008256.ref018","unstructured":"Pachitariu M, Steinmetz NA, Kadir SN, Carandini M, Harris KD. Fast and accurate spike sorting of high-channel count probes with KiloSort. In: Advances in neural information processing systems; 2016. p. 4448\u20134456."},{"issue":"5","key":"pcbi.1008256.ref019","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1016\/j.neuron.2016.07.036","article-title":"High-throughput mapping of single-neuron projections by sequencing of barcoded RNA","volume":"91","author":"JM Kebschull","year":"2016","journal-title":"Neuron"},{"issue":"7699","key":"pcbi.1008256.ref020","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nature26159","article-title":"The logic of single-cell projections from visual cortex","volume":"556","author":"Y Han","year":"2018","journal-title":"Nature"},{"issue":"4","key":"pcbi.1008256.ref021","doi-asserted-by":"crossref","first-page":"e22","DOI":"10.1093\/nar\/gkx1206","article-title":"Efficient in situ barcode sequencing using padlock probe-based BaristaSeq","volume":"46","author":"X Chen","year":"2018","journal-title":"Nucleic acids research"},{"key":"pcbi.1008256.ref022","article-title":"YASS: Yet Another Spike Sorter applied to large-scale multi-electrode array recordings in primate retina","author":"J Lee","year":"2020","journal-title":"bioRxiv"},{"key":"pcbi.1008256.ref023","unstructured":"Gershman S, Goodman N. Amortized inference in probabilistic reasoning. In: Proceedings of the annual meeting of the cognitive science society. vol. 36; 2014."},{"key":"pcbi.1008256.ref024","unstructured":"Marino J, Yue Y, Mandt S. Iterative amortized inference. arXiv preprint arXiv:180709356. 2018."}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1008256","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,3,18]],"date-time":"2021-03-18T00:00:00Z","timestamp":1616025600000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008256","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,3,18]],"date-time":"2021-03-18T14:14:40Z","timestamp":1616076880000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008256"}},"subtitle":[],"editor":[{"given":"Emma Claire","family":"Robinson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,3,8]]},"references-count":24,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2021,3,8]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1008256","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.08.17.253666","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,3,8]]}}}