{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T15:32:07Z","timestamp":1793719927550,"version":"4.6.1"},"reference-count":30,"publisher":"Springer Science and Business Media LLC","issue":"11","license":[{"start":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T00:00:00Z","timestamp":1781654400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T00:00:00Z","timestamp":1781654400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Protoc"],"published-print":{"date-parts":[[2026,11]]},"DOI":"10.1038\/s41596-026-01386-2","type":"journal-article","created":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T11:30:21Z","timestamp":1781695821000},"page":"5456-5490","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Whole-organ spatial transcriptional analysis at cellular resolution using TRISCO"],"prefix":"10.1038","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0584-1119","authenticated-orcid":false,"given":"Yue","family":"Li","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-3781-4972","authenticated-orcid":false,"given":"Abigail","family":"Walton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Judith C.","family":"Kreutzmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-1397-1585","authenticated-orcid":false,"given":"Lea","family":"Lydolph Larsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1567-3078","authenticated-orcid":false,"given":"Ilse","family":"Eidhof","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob Lercke","family":"Skytte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Casper Gravesen","family":"Salinas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Urmas","family":"Roostalu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob","family":"Hecksher-S\u00f8rensen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2226-4288","authenticated-orcid":false,"given":"Shigeaki","family":"Kanatani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1446-1062","authenticated-orcid":false,"given":"Per","family":"Uhl\u00e9n","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,17]]},"reference":[{"key":"1386_CR1","doi-asserted-by":"publisher","first-page":"1153","DOI":"10.1038\/s41592-024-02327-1","volume":"21","author":"A Ert\u00fcrk","year":"2024","unstructured":"Ert\u00fcrk, A. Deep 3D histology powered by tissue clearing, omics and AI. Nat. Methods 21, 1153\u20131165 (2024).","journal-title":"Nat. Methods"},{"key":"1386_CR2","doi-asserted-by":"publisher","first-page":"896","DOI":"10.1016\/j.cell.2014.10.010","volume":"159","author":"N Renier","year":"2014","unstructured":"Renier, N. et al. iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging. Cell 159, 896\u2013910 (2014).","journal-title":"Cell"},{"key":"1386_CR3","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1016\/j.cell.2014.03.042","volume":"157","author":"EA Susaki","year":"2014","unstructured":"Susaki, E. A. et al. Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell 157, 726\u2013739 (2014).","journal-title":"Cell"},{"key":"1386_CR4","doi-asserted-by":"publisher","DOI":"10.1016\/j.crmeth.2023.100458","volume":"3","author":"CN Yau","year":"2023","unstructured":"Yau, C. N. et al. Principles of deep immunohistochemistry for 3D histology. Cell Rep. Methods 3, 100458 (2023).","journal-title":"Cell Rep. Methods"},{"key":"1386_CR5","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1126\/science.adn9947","volume":"386","author":"S Kanatani","year":"2024","unstructured":"Kanatani, S. et al. Whole-brain spatial transcriptional analysis at cellular resolution. Science 386, 907\u2013915 (2024).","journal-title":"Science"},{"key":"1386_CR6","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1038\/nm.2600","volume":"18","author":"A Ert\u00fcrk","year":"2012","unstructured":"Ert\u00fcrk, A. et al. Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury. Nat. Med. 18, 166\u2013171 (2012).","journal-title":"Nat. Med."},{"key":"1386_CR7","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1038\/nature12107","volume":"497","author":"K Chung","year":"2013","unstructured":"Chung, K. et al. Structural and molecular interrogation of intact biological systems. Nature 497, 332\u2013337 (2013).","journal-title":"Nature"},{"key":"1386_CR8","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1038\/nmeth1036","volume":"4","author":"HU Dodt","year":"2007","unstructured":"Dodt, H. U. et al. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat. Methods 4, 331\u2013336 (2007).","journal-title":"Nat. Methods"},{"key":"1386_CR9","doi-asserted-by":"publisher","first-page":"792","DOI":"10.1016\/j.cell.2016.01.038","volume":"164","author":"EL Sylwestrak","year":"2016","unstructured":"Sylwestrak, E. L., Rajasethupathy, P., Wright, M. A., Jaffe, A. & Deisseroth, K. Multiplexed intact-tissue transcriptional analysis at cellular resolution. Cell 164, 792\u2013804 (2016).","journal-title":"Cell"},{"key":"1386_CR10","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1016\/j.neuroimage.2007.05.046","volume":"37","author":"A Badea","year":"2007","unstructured":"Badea, A., Ali-Sharief, A. A. & Johnson, G. A. Morphometric analysis of the C57BL\/6J mouse brain. Neuroimage 37, 683\u2013693 (2007).","journal-title":"Neuroimage"},{"key":"1386_CR11","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1038\/s41551-020-0576-z","volume":"4","author":"N Tanaka","year":"2020","unstructured":"Tanaka, N. et al. Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies. Nat. Biomed. Eng. 4, 875\u2013888 (2020).","journal-title":"Nat. Biomed. Eng."},{"key":"1386_CR12","doi-asserted-by":"publisher","first-page":"dev165753","DOI":"10.1242\/dev.165753","volume":"145","author":"HMT Choi","year":"2018","unstructured":"Choi, H. M. T. et al. Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust. Development 145, dev165753 (2018).","journal-title":"Development"},{"key":"1386_CR13","doi-asserted-by":"publisher","first-page":"1079","DOI":"10.1152\/physrev.00013.2009","volume":"89","author":"S Loebrich","year":"2009","unstructured":"Loebrich, S. & Nedivi, E. The function of activity-regulated genes in the nervous system. Physiol. Rev. 89, 1079\u20131103 (2009).","journal-title":"Physiol. Rev."},{"key":"1386_CR14","doi-asserted-by":"publisher","first-page":"1789","DOI":"10.1016\/j.cell.2016.05.007","volume":"165","author":"N Renier","year":"2016","unstructured":"Renier, N. et al. Mapping of brain activity by automated volume analysis of immediate early genes. Cell 165, 1789\u20131802 (2016).","journal-title":"Cell"},{"key":"1386_CR15","doi-asserted-by":"publisher","unstructured":"Murakami, T. C. & Heintz, N. Multiplexed and scalable cellular phenotyping toward the standardized three-dimensional human neuroanatomy. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.11.23.517711 (2022).","DOI":"10.1101\/2022.11.23.517711"},{"key":"1386_CR16","doi-asserted-by":"publisher","first-page":"1380","DOI":"10.1016\/j.neuron.2025.12.027","volume":"114","author":"TC Murakami","year":"2026","unstructured":"Murakami, T. C. et al. Artificial intelligence-driven whole-brain cell mapping with highly multiplexed in situ hybridization. Neuron 114, 1380\u20131398.e9 (2026).","journal-title":"Neuron"},{"key":"1386_CR17","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature13186","volume":"508","author":"SW Oh","year":"2014","unstructured":"Oh, S. W. et al. A mesoscale connectome of the mouse brain. Nature 508, 207\u2013214 (2014).","journal-title":"Nature"},{"key":"1386_CR18","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1016\/j.cell.2014.07.017","volume":"158","author":"B Yang","year":"2014","unstructured":"Yang, B. et al. Single-cell phenotyping within transparent intact tissue through whole-body clearing. Cell 158, 945\u2013958 (2014).","journal-title":"Cell"},{"key":"1386_CR19","doi-asserted-by":"publisher","first-page":"911","DOI":"10.1016\/j.cell.2014.10.034","volume":"159","author":"K Tainaka","year":"2014","unstructured":"Tainaka, K. et al. Whole-body imaging with single-cell resolution by tissue decolorization. Cell 159, 911\u2013924 (2014).","journal-title":"Cell"},{"key":"1386_CR20","doi-asserted-by":"publisher","first-page":"883","DOI":"10.15252\/msb.20167144","volume":"12","author":"F Edfors","year":"2016","unstructured":"Edfors, F. et al. Gene-specific correlation of RNA and protein levels in human cells and tissues. Mol. Syst. Biol. 12, 883 (2016).","journal-title":"Mol. Syst. Biol."},{"key":"1386_CR21","doi-asserted-by":"publisher","first-page":"e0124650","DOI":"10.1371\/journal.pone.0124650","volume":"10","author":"MK Schwarz","year":"2015","unstructured":"Schwarz, M. K. et al. Fluorescent-protein stabilization and high-resolution imaging of cleared, intact mouse brains. PLoS ONE 10, e0124650 (2015).","journal-title":"PLoS ONE"},{"key":"1386_CR22","doi-asserted-by":"publisher","DOI":"10.1002\/jbio.201800368","volume":"12","author":"C Hahn","year":"2019","unstructured":"Hahn, C. et al. High-resolution imaging of fluorescent whole mouse brains using stabilised organic media (sDISCO). J. Biophotonics 12, e201800368 (2019).","journal-title":"J. Biophotonics"},{"key":"1386_CR23","doi-asserted-by":"publisher","first-page":"9637","DOI":"10.3390\/ijms23179637","volume":"23","author":"T Lu","year":"2022","unstructured":"Lu, T., Shinozaki, M., Nagoshi, N., Nakamura, M. & Okano, H. Long preservation of AAV-transduced fluorescence by a modified organic solvent-based clearing method. Int. J. Mol. Sci. 23, 9637 (2022).","journal-title":"Int. J. Mol. Sci."},{"key":"1386_CR24","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1016\/j.ijbiomac.2008.05.002","volume":"43","author":"AA Alnuami","year":"2008","unstructured":"Alnuami, A. A., Zeedi, B., Qadri, S. M. & Ashraf, S. S. Oxyradical-induced GFP damage and loss of fluorescence. Int. J. Biol. Macromol. 43, 182\u2013186 (2008).","journal-title":"Int. J. Biol. Macromol."},{"key":"1386_CR25","doi-asserted-by":"publisher","first-page":"15275","DOI":"10.1073\/pnas.0407024101","volume":"101","author":"RM Dirks","year":"2004","unstructured":"Dirks, R. M. & Pierce, N. A. Triggered amplification by hybridization chain reaction. Proc. Natl Acad. Sci. USA 101, 15275\u201315278 (2004).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1386_CR26","doi-asserted-by":"publisher","first-page":"1208","DOI":"10.1038\/nbt.1692","volume":"28","author":"HM Choi","year":"2010","unstructured":"Choi, H. M. et al. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat. Biotechnol. 28, 1208\u20131212 (2010).","journal-title":"Nat. Biotechnol."},{"key":"1386_CR27","doi-asserted-by":"publisher","first-page":"4284","DOI":"10.1021\/nn405717p","volume":"8","author":"HM Choi","year":"2014","unstructured":"Choi, H. M., Beck, V. A. & Pierce, N. A. Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability. ACS Nano 8, 4284\u20134294 (2014).","journal-title":"ACS Nano"},{"key":"1386_CR28","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1007\/978-1-0716-1119-7_6","volume":"2245","author":"C de Charleroy","year":"2021","unstructured":"de Charleroy, C., Haseeb, A. & Lefebvre, V. Preparation of adult mouse skeletal tissue sections for RNA in situ hybridization. Methods Mol. Biol. 2245, 85\u201392 (2021).","journal-title":"Methods Mol. Biol."},{"key":"1386_CR29","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-13-316","volume":"13","author":"A Bria","year":"2012","unstructured":"Bria, A. & Iannello, G. TeraStitcher\u2014a tool for fast automatic 3D-stitching of teravoxel-sized microscopy images. BMC Bioinformatics 13, 316 (2012).","journal-title":"BMC Bioinformatics"},{"key":"1386_CR30","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1007\/s12021-020-09490-8","volume":"19","author":"J Perens","year":"2021","unstructured":"Perens, J. et al. An optimized mouse brain atlas for automated mapping and quantification of neuronal activity using iDISCO+ and light sheet fluorescence microscopy. Neuroinformatics 19, 433\u2013446 (2021).","journal-title":"Neuroinformatics"}],"container-title":["Nature Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41596-026-01386-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41596-026-01386-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41596-026-01386-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T15:02:15Z","timestamp":1793718135000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41596-026-01386-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,17]]},"references-count":30,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2026,11]]}},"alternative-id":["1386"],"URL":"https:\/\/doi.org\/10.1038\/s41596-026-01386-2","relation":{},"ISSN":["1754-2189","1750-2799"],"issn-type":[{"value":"1754-2189","type":"print"},{"value":"1750-2799","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,17]]},"assertion":[{"value":"15 August 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 April 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 June 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"L.L.L., J.L.S., C.G.S., U.R. and J.H.-S. are employees and hold shares at Gubra ApS.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}]}}