{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T16:28:01Z","timestamp":1793550481936,"version":"4.5.0"},"reference-count":18,"publisher":"Elsevier BV","issue":"4","license":[{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T00:00:00Z","timestamp":1788307200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/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\/100007231","name":"Cornell University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007231","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100022388","name":"Howard Hughes Medical Institute Janelia Research Campus","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100022388","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["STAR Protocols"],"published-print":{"date-parts":[[2026,12]]},"DOI":"10.1016\/j.xpro.2026.104848","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T23:47:39Z","timestamp":1790812059000},"page":"104848","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Protocol for correlating in vivo calcium imaging with spatial transcriptomics in the mouse brain"],"prefix":"10.1016","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9717-6763","authenticated-orcid":false,"given":"Risa","family":"Yamazaki","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0280-8137","authenticated-orcid":false,"given":"Mark","family":"Eddison","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-0376-5116","authenticated-orcid":false,"given":"Anja","family":"Payne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4447-5043","authenticated-orcid":false,"given":"Yuhan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.xpro.2026.104848_bib1","article-title":"A Scalable Cross-Modal Workflow for Linking In Vivo Neural Activity to Neuronal Cell Types via Spatial Gene Profiling","author":"Yamazaki","year":"2026","journal-title":"bioRxiv"},{"key":"10.1016\/j.xpro.2026.104848_bib2","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/s41586-023-06818-7","article-title":"The molecular cytoarchitecture of the adult mouse brain","volume":"624","author":"Langlieb","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.xpro.2026.104848_bib3","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/s41586-023-06569-5","article-title":"Spatial atlas of the mouse central nervous system at molecular resolution","volume":"622","author":"Shi","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.xpro.2026.104848_bib4","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1038\/s41586-023-06812-z","article-title":"A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain","volume":"624","author":"Yao","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.xpro.2026.104848_bib5","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/s41586-023-06808-9","article-title":"Molecularly defined and spatially resolved cell atlas of the whole mouse brain","volume":"624","author":"Zhang","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.xpro.2026.104848_bib6","doi-asserted-by":"crossref","first-page":"6361","DOI":"10.1016\/j.cell.2021.11.024","article-title":"EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization","volume":"184","author":"Wang","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.xpro.2026.104848_bib7","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/nrn2338","article-title":"Imaging in vivo: watching the brain in action","volume":"9","author":"Kerr","year":"2008","journal-title":"Nat. Rev. Neurosci."},{"key":"10.1016\/j.xpro.2026.104848_bib8","article-title":"Multimodal mapping of cell types and projections in the central nucleus of the amygdala","volume":"12","author":"Wang","year":"2023","journal-title":"eLife"},{"key":"10.1016\/j.xpro.2026.104848_bib9","article-title":"Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx)","volume":"11","author":"Damstra","year":"2022","journal-title":"eLife"},{"key":"10.1016\/j.xpro.2026.104848_bib10","doi-asserted-by":"crossref","DOI":"10.21769\/BioProtoc.3988","article-title":"Transcardiac Perfusion of the Mouse for Brain Tissue Dissection and Fixation","volume":"11","author":"Wu","year":"2021","journal-title":"Bio. Protoc."},{"key":"10.1016\/j.xpro.2026.104848_bib11","series-title":"Robust registration of calcium images by learned contrast synthesis","first-page":"1123","author":"Bogovic","year":"2016"},{"key":"10.1016\/j.xpro.2026.104848_bib12","article-title":"Extracting large-scale neural activity with Suite2p","author":"Stringer","year":"2026","journal-title":"bioRxiv"},{"key":"10.1016\/j.xpro.2026.104848_bib13","doi-asserted-by":"crossref","DOI":"10.1242\/dev.165753","article-title":"Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust","volume":"145","author":"Choi","year":"2018","journal-title":"Development"},{"key":"10.1016\/j.xpro.2026.104848_bib14","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.conb.2017.05.014","article-title":"Genetic strategies to access activated neurons","volume":"45","author":"DeNardo","year":"2017","journal-title":"Curr. Opin. Neurobiol."},{"key":"10.1016\/j.xpro.2026.104848_bib15","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1038\/s41593-020-0655-1","article-title":"Multiple convergent hypothalamus-brainstem circuits drive defensive behavior","volume":"23","author":"Lovett-Barron","year":"2020","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.xpro.2026.104848_bib16","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1038\/s41586-024-08518-2","article-title":"Transcriptomic neuron types vary topographically in function and morphology","volume":"638","author":"Shainer","year":"2025","journal-title":"Nature"},{"key":"10.1016\/j.xpro.2026.104848_bib17","article-title":"Whole-Brain Co-Mapping of Gene Expression and Neuronal Activity at Cellular Resolution in Behaving Zebrafish","author":"Marquez-Legorreta","year":"2026","journal-title":"bioRxiv"},{"key":"10.1016\/j.xpro.2026.104848_bib18","doi-asserted-by":"crossref","DOI":"10.3791\/67656","article-title":"Multiplex Detection of Gene Expression in the Intact Drosophila Brain Using Expansion-Assisted Iterative Fluorescence In Situ Hybridization","author":"Close","year":"2025","journal-title":"J. Vis. Exp."}],"container-title":["STAR Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666166726005010?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666166726005010?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T15:41:35Z","timestamp":1793547695000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2666166726005010"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,12]]},"references-count":18,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["S2666166726005010"],"URL":"https:\/\/doi.org\/10.1016\/j.xpro.2026.104848","relation":{},"ISSN":["2666-1667"],"issn-type":[{"value":"2666-1667","type":"print"}],"subject":[],"published":{"date-parts":[[2026,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Protocol for correlating in vivo calcium imaging with spatial transcriptomics in the mouse brain","name":"articletitle","label":"Article Title"},{"value":"STAR Protocols","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.xpro.2026.104848","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"104848"}}