{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T06:10:45Z","timestamp":1792649445593,"version":"4.5.0"},"reference-count":39,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,2,13]],"date-time":"2023-02-13T00:00:00Z","timestamp":1676246400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,2,13]],"date-time":"2023-02-13T00:00:00Z","timestamp":1676246400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Commun Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The ability to image human tissue samples in 3D, with both cellular resolution and a large field of view (FOV), can improve fundamental and clinical investigations. Here, we demonstrate the feasibility of light-sheet imaging of ~5 cm\n                    <jats:sup>3<\/jats:sup>\n                    sized formalin fixed human brain and up to ~7 cm\n                    <jats:sup>3<\/jats:sup>\n                    sized formalin fixed paraffin embedded (FFPE) prostate cancer samples, processed with the FFPE-MASH protocol. We present a light-sheet microscopy prototype, the cleared-tissue dual view Selective Plane Illumination Microscope (ct-dSPIM), capable of fast 3D high-resolution acquisitions of cm\n                    <jats:sup>3<\/jats:sup>\n                    scale cleared tissue. We used mosaic scans for fast 3D overviews of entire tissue samples or higher resolution overviews of large ROIs with various speeds: (a) Mosaic 16 (16.4\u2009\u00b5m isotropic resolution, ~1.7\u2009h\/cm\n                    <jats:sup>3<\/jats:sup>\n                    ), (b) Mosaic 4 (4.1\u2009\u00b5m isotropic resolution, ~ 5\u2009h\/cm\n                    <jats:sup>3<\/jats:sup>\n                    ) and (c) Mosaic 0.5 (0.5\u2009\u00b5m near isotropic resolution, ~15.8\u2009h\/cm\n                    <jats:sup>3<\/jats:sup>\n                    ). We could visualise cortical layers and neurons around the border of human brain areas V1&amp;V2, and could demonstrate suitable imaging quality for Gleason score grading in thick prostate cancer samples. We show that ct-dSPIM imaging is an excellent technique to quantitatively assess entire MASH prepared large-scale human tissue samples in 3D, with considerable future clinical potential.\n                  <\/jats:p>","DOI":"10.1038\/s42003-023-04536-4","type":"journal-article","created":{"date-parts":[[2023,2,13]],"date-time":"2023-02-13T08:05:38Z","timestamp":1676275538000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":43,"title":["Efficient 3D light-sheet imaging of very large-scale optically cleared human brain and prostate tissue samples"],"prefix":"10.1038","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8303-7495","authenticated-orcid":false,"given":"Anna","family":"Schueth","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3783-8213","authenticated-orcid":false,"given":"Sven","family":"Hildebrand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4092-0672","authenticated-orcid":false,"given":"Iryna","family":"Samarska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shubharthi","family":"Sengupta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annemarie","family":"Kiessling","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Herrler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Axel","family":"zur Hausen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Capalbo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alard","family":"Roebroeck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,2,13]]},"reference":[{"key":"4536_CR1","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1016\/j.cbpa.2021.05.003","volume":"63","author":"S Munck","year":"2021","unstructured":"Munck, S. et al. Maximizing content across scales: moving multimodal microscopy and mesoscopy toward molecular imaging. Curr. Opin. Chem. Biol. 63, 188\u2013199 (2021).","journal-title":"Curr. Opin. Chem. Biol."},{"key":"4536_CR2","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1016\/j.cell.2015.09.029","volume":"163","author":"H Markram","year":"2015","unstructured":"Markram, H. Reconstruction and simulation of neocortical microcircuitry. Cell, Oktober 163, 456\u2013492 (2015).","journal-title":"Cell, Oktober"},{"key":"4536_CR3","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1097\/PAS.0000000000000530","volume":"40","author":"JI Epstein","year":"2016","unstructured":"Epstein, J. I. et al. The 2014 International Society of Urological Pathology (ISUP) consensus conference on gleason grading of prostatic carcinoma: definition of grading patterns and proposal for a new grading system. Am. J. Surg. Pathol. 40, 244\u2013252 (2016).","journal-title":"Am. J. Surg. Pathol."},{"key":"4536_CR4","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/j.media.2018.09.005","volume":"50","author":"G Nir","year":"2018","unstructured":"Nir, G. et al. Automatic grading of prostate cancer in digitized histopathology images: learning from multiple experts. Med. Image Anal. 50, 167\u2013180 (2018).","journal-title":"Med. Image Anal."},{"key":"4536_CR5","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1177\/1066896920907690","volume":"28","author":"AT Paulk","year":"2020","unstructured":"Paulk, A. T., Sesterhenn, I. A. & Burke, A. P. Recutting blocks of prostate needle biopsies: how much diagnostic yield is gained? Int J. Surg. Pathol. 28, 490\u2013495 (2020).","journal-title":"Int J. Surg. Pathol."},{"key":"4536_CR6","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":"4536_CR7","doi-asserted-by":"publisher","first-page":"1138","DOI":"10.1016\/j.celrep.2016.06.060","volume":"16","author":"T Liebmann","year":"2016","unstructured":"Liebmann, T. et al. Three-dimensional study of Alzheimer\u2019s disease Hallmarks using the iDISCO clearing method. Cell Rep. 16, 1138\u20131152 (2016).","journal-title":"Cell Rep."},{"key":"4536_CR8","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1111\/nan.12293","volume":"42","author":"AK Liu","year":"2016","unstructured":"Liu, A. K. et al. Bringing CLARITY to the human brain: visualization of Lewy pathology in three dimensions. Neuropathol. Appl. Neurobiol. 42, 573\u2013587 (2016).","journal-title":"Neuropathol. Appl. Neurobiol."},{"key":"4536_CR9","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":"4536_CR10","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":"4536_CR11","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-71737-w","volume":"10","author":"I Sabdyusheva Litschauer","year":"2020","unstructured":"Sabdyusheva Litschauer, I. et al. 3D histopathology of human tumours by fast clearing and ultramicroscopy. Sci. Rep. 10, 17619 (2020).","journal-title":"Sci. Rep."},{"key":"4536_CR12","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15906-5","volume":"11","author":"EA Susaki","year":"2020","unstructured":"Susaki, E. A. et al. Versatile whole-organ\/body staining and imaging based on electrolyte-gel properties of biological tissues. Nat. Commun. 11, 1982 (2020).","journal-title":"Nat. Commun."},{"key":"4536_CR13","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1038\/s42003-022-03390-0","volume":"5","author":"L Pesce","year":"2022","unstructured":"Pesce, L. et al. 3D molecular phenotyping of cleared human brain tissues with light-sheet fluorescence microscopy. Commun. Biol. 5, 447 (2022).","journal-title":"Commun. Biol."},{"key":"4536_CR14","doi-asserted-by":"publisher","first-page":"796","DOI":"10.1016\/j.cell.2020.01.030","volume":"180","author":"S Zhao","year":"2020","unstructured":"Zhao, S. et al. Cellular and molecular probing of intact human Organs. Cell 180, 796\u2013812.e19 (2020).","journal-title":"Cell"},{"key":"4536_CR15","doi-asserted-by":"publisher","DOI":"10.1038\/srep09808","volume":"5","author":"I Costantini","year":"2015","unstructured":"Costantini, I. et al. A versatile clearing agent for multi-modal brain imaging. Sci. Rep. 5, 9808 (2015).","journal-title":"Sci. Rep."},{"key":"4536_CR16","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-018-0521-8","volume":"16","author":"B Migliori","year":"2018","unstructured":"Migliori, B. et al. Light sheet theta microscopy for rapid high-resolution imaging of large biological samples. BMC Biol. 16, 57 (2018).","journal-title":"BMC Biol."},{"key":"4536_CR17","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-10534-0","volume":"10","author":"AK Glaser","year":"2019","unstructured":"Glaser, A. K. et al. Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues. Nat. Commun. 10, 2781 (2019).","journal-title":"Nat. Commun."},{"key":"4536_CR18","doi-asserted-by":"publisher","first-page":"1337","DOI":"10.1038\/s41587-020-0560-x","volume":"38","author":"M Guo","year":"2020","unstructured":"Guo, M. et al. Rapid image deconvolution and multiview fusion for optical microscopy. Nat. Biotechnol. 38, 1337\u20131346 (2020).","journal-title":"Nat. Biotechnol."},{"key":"4536_CR19","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-47336-9","volume":"9","author":"S Hildebrand","year":"2019","unstructured":"Hildebrand, S. et al. Scalable labeling for cytoarchitectonic characterization of large optically cleared human neocortex samples. Sci. Rep. 9, 10880 (2019).","journal-title":"Sci. Rep."},{"key":"4536_CR20","doi-asserted-by":"publisher","first-page":"1427","DOI":"10.1038\/s41592-022-01652-7","volume":"19","author":"Y Li","year":"2022","unstructured":"Li, Y. et al. Incorporating the image formation process into deep learning improves network performance. Nat. Methods 19, 1427\u20131437 (2022).","journal-title":"Nat. Methods"},{"key":"4536_CR21","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1038\/s41592-019-0554-0","volume":"16","author":"FF Voigt","year":"2019","unstructured":"Voigt, F. F. et al. The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue. Nat. Methods 16, 1105\u20131108 (2019).","journal-title":"Nat. Methods"},{"key":"4536_CR22","doi-asserted-by":"publisher","DOI":"10.1038\/s41377-020-00401-9","volume":"9","author":"T Chakraborty","year":"2020","unstructured":"Chakraborty, T. et al. Converting lateral scanning into axial focusing to speed up three-dimensional microscopy. Light Sci. Appl 9, 165 (2020).","journal-title":"Light Sci. Appl"},{"key":"4536_CR23","doi-asserted-by":"publisher","first-page":"2518","DOI":"10.1523\/JNEUROSCI.4526-04.2005","volume":"25","author":"S Herculano-Houzel","year":"2005","unstructured":"Herculano-Houzel, S. & Lent, R. Isotropic fractionator: a simple, rapid method for the quantification of total cell and neuron numbers in the brain. J. Neurosci. 25, 2518\u20132521 (2005).","journal-title":"J. Neurosci."},{"key":"4536_CR24","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1007\/BF00250564","volume":"77","author":"G Leuba","year":"1989","unstructured":"Leuba, G. & Garey, L. J. Comparison of neuronal and glial numerical density in primary and secondary visual cortex of man. Exp. Brain Res. 77, 31\u201338 (1989).","journal-title":"Exp. Brain Res."},{"key":"4536_CR25","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1038\/nmeth.3964","volume":"13","author":"C Pan","year":"2016","unstructured":"Pan, C. et al. Shrinkage-mediated imaging of entire organs and organisms using uDISCO. Nat. Methods 13, 859\u2013867 (2016).","journal-title":"Nat. Methods"},{"key":"4536_CR26","doi-asserted-by":"publisher","first-page":"118832","DOI":"10.1016\/j.neuroimage.2021.118832","volume":"247","author":"H Rusch","year":"2022","unstructured":"Rusch, H. et al. Finding the best clearing approach\u2014towards 3D wide-scale multimodal imaging of aged human brain tissue. Neuroimage 247, 118832 (2022).","journal-title":"Neuroimage"},{"key":"4536_CR27","doi-asserted-by":"publisher","first-page":"2188","DOI":"10.1038\/s41596-022-00712-8","volume":"17","author":"H Mai","year":"2022","unstructured":"Mai, H. et al. Scalable tissue labeling and clearing of intact human organs. Nat. Protoc. 17, 2188\u20132215 (2022).","journal-title":"Nat. Protoc."},{"key":"4536_CR28","doi-asserted-by":"publisher","first-page":"0084","DOI":"10.1038\/s41551-017-0084","volume":"1","author":"AK Glaser","year":"2017","unstructured":"Glaser, A. K. et al. Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens. Nat. Biomed. Eng. 1, 0084 (2017).","journal-title":"Nat. Biomed. Eng."},{"key":"4536_CR29","unstructured":"Federa. Human Tissue and Medical Research: Code of Conduct for Responsible Use (Committee for Guidelines in Research COREON, 2011)."},{"key":"4536_CR30","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1016\/S0021-9258(18)86000-8","volume":"49","author":"TC McIlvaine","year":"1921","unstructured":"McIlvaine, T. C. A buffer solution for colorimetric comparison. J. Biol. Chem. 49, 183\u2013186 (1921).","journal-title":"J. Biol. Chem."},{"key":"4536_CR31","doi-asserted-by":"publisher","first-page":"2555","DOI":"10.1038\/nprot.2014.172","volume":"9","author":"A Kumar","year":"2014","unstructured":"Kumar, A. et al. Dual-view plane illumination microscopy for rapid and spatially isotropic imaging. Nat. Protoc. 9, 2555\u20132573 (2014).","journal-title":"Nat. Protoc."},{"key":"4536_CR32","doi-asserted-by":"publisher","first-page":"e10","DOI":"10.14440\/jbm.2014.36","volume":"1","author":"AD Edelstein","year":"2014","unstructured":"Edelstein, A. D. et al. Advanced methods of microscope control using \u03bcManager software. J. Biol. Methods 1, e10 (2014).","journal-title":"J. Biol. Methods"},{"key":"4536_CR33","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676\u2013682 (2012).","journal-title":"Nat. Methods"},{"key":"4536_CR34","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1038\/s41592-019-0501-0","volume":"16","author":"D Horl","year":"2019","unstructured":"Horl, D. et al. BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples. Nat. Methods 16, 870\u2013874 (2019).","journal-title":"Nat. Methods"},{"key":"4536_CR35","doi-asserted-by":"publisher","first-page":"1109","DOI":"10.1038\/s41592-019-0615-4","volume":"16","author":"T Chakraborty","year":"2019","unstructured":"Chakraborty, T. et al. Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution. Nat. Methods 16, 1109\u20131113 (2019).","journal-title":"Nat. Methods"},{"key":"4536_CR36","doi-asserted-by":"publisher","unstructured":"Glaser, A. K. et al. A hybrid open-top light-sheet microscope for multi-scale imaging of cleared tissues. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2020.05.06.081745 (2021).","DOI":"10.1101\/2020.05.06.081745"},{"key":"4536_CR37","doi-asserted-by":"publisher","first-page":"1032","DOI":"10.1038\/nbt.2713","volume":"31","author":"Y Wu","year":"2013","unstructured":"Wu, Y. et al. Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. Nat. Biotechnol. 31, 1032\u20131038 (2013).","journal-title":"Nat. Biotechnol."},{"key":"4536_CR38","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1038\/nphoton.2014.323","volume":"9","author":"MB Bouchard","year":"2015","unstructured":"Bouchard, M. B. et al. Swept confocally-aligned planar excitation (SCAPE) microscopy for high speed volumetric imaging of behaving organisms. Nat. Photonics 9, 113\u2013119 (2015).","journal-title":"Nat. Photonics"},{"key":"4536_CR39","doi-asserted-by":"publisher","first-page":"1497","DOI":"10.1364\/OE.27.001497","volume":"27","author":"L Gao","year":"2019","unstructured":"Gao, L. et al. Lattice light sheet microscopy using tiling lattice light sheets. Opt. Express 27, 1497\u20131506 (2019).","journal-title":"Opt. Express"}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-023-04536-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-023-04536-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-023-04536-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,13]],"date-time":"2023-02-13T21:04:45Z","timestamp":1676322285000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-023-04536-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,13]]},"references-count":39,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["4536"],"URL":"https:\/\/doi.org\/10.1038\/s42003-023-04536-4","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.07.14.500098","asserted-by":"object"}]},"ISSN":["2399-3642"],"issn-type":[{"value":"2399-3642","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,2,13]]},"assertion":[{"value":"26 July 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 January 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 February 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"170"}}