{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T10:37:07Z","timestamp":1787567827242,"version":"build-2736575974"},"reference-count":21,"publisher":"eLife Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2025,4,7]],"date-time":"2025-04-07T00:00:00Z","timestamp":1743984000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,4,7]],"date-time":"2025-04-07T00:00:00Z","timestamp":1743984000000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,4,7]],"date-time":"2025-04-07T00:00:00Z","timestamp":1743984000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFA0806400"],"award-info":[{"award-number":["2022YFA0806400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Guangzhou Key Research Program on Brain Science","award":["202206060001"],"award-info":[{"award-number":["202206060001"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82130068"],"award-info":[{"award-number":["82130068"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elifesciences.org"],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>The increasing use of tissue clearing techniques underscores the urgent need for cost-effective and simplified deep imaging methods. While traditional inverted confocal microscopes excel in high-resolution imaging of tissue sections and cultured cells, they face limitations in deep imaging of cleared tissues due to refractive index mismatches between the immersion media of objectives and sample container. To overcome these challenges, the RIM-Deep was developed to significantly improve deep imaging capabilities without compromising the normal function of the confocal microscope. This system facilitates deep immunofluorescence imaging of the prefrontal cortex in cleared macaque tissue, extending imaging depth from 2 mm to 5 mm. Applied to an intact and cleared Thy1-EGFP mouse brain, the system allowed for clear axonal visualization at high imaging depth. Moreover, this advancement enables large-scale, deep 3D imaging of intact tissues. In principle, this concept can be extended to any imaging modality, including existing inverted wide-field, confocal, and two-photon microscopy. This would significantly upgrade traditional laboratory configurations and facilitate the study of connectomes in the brain and other tissues.<\/jats:p>","DOI":"10.7554\/elife.101143","type":"journal-article","created":{"date-parts":[[2024,10,14]],"date-time":"2024-10-14T06:25:24Z","timestamp":1728887124000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.101143","source":"Crossref","is-referenced-by-count":0,"title":["A novel method (RIM-Deep) for enhancing imaging depth and resolution stability of deep cleared tissue in inverted confocal microscopy"],"prefix":"10.7554","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2121-8557","authenticated-orcid":true,"given":"Yisi","family":"Liu","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01vjw4z39","id-type":"ROR","asserted-by":"publisher"}],"name":"Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University","place":["Guangzhou, China"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Pu","family":"Wang","sequence":"additional","affiliation":[{"name":"Nikon Precision Corporation, Guangzhou , China","place":["Shanghai, China"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Junjie","family":"Zou","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01vjw4z39","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, The National Key Clinical Specialty","place":["Guangzhou, China"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"methodology","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2472-8541","authenticated-orcid":true,"given":"Hongwei","family":"Zhou","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01vjw4z39","id-type":"ROR","asserted-by":"publisher"}],"name":"Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University","place":["Guangzhou, China"]},{"id":[{"id":"https:\/\/ror.org\/01vjw4z39","id-type":"ROR","asserted-by":"publisher"}],"name":"State Key Laboratory of Organ Failure Research, Southern Medical University","place":["Guangzhou, China"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"4374","published-online":{"date-parts":[[2025,4,7]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-03743-4","type":"journal-article","article-title":"Super-resolution microscopy with very large working distance by means of distributed aperture illumination","volume":"7","author":"Birk","year":"2017","journal-title":"Scientific Reports"},{"key":"bib2","doi-asserted-by":"publisher","first-page":"2773","DOI":"10.1038\/s41596-020-0360-2","type":"journal-article","article-title":"Tutorial: avoiding and correcting sample-induced spherical aberration artifacts in 3D fluorescence microscopy","volume":"15","author":"Diel","year":"2020","journal-title":"Nature Protocols"},{"key":"bib3","doi-asserted-by":"publisher","DOI":"10.1117\/1.NPh.2.4.041407","type":"journal-article","article-title":"Ultramicroscopy: development and outlook","volume":"2","author":"Dodt","year":"2015","journal-title":"Neurophotonics"},{"key":"bib4","doi-asserted-by":"publisher","DOI":"10.1002\/cpcy.68","type":"journal-article","article-title":"Confocal microscopy: principles and modern practices","volume":"92","author":"Elliott","year":"2020","journal-title":"Current Protocols in Cytometry"},{"key":"bib5","doi-asserted-by":"publisher","first-page":"1477","DOI":"10.1364\/ol.31.001477","type":"journal-article","article-title":"Resolution enhancement in a light-sheet-based microscope (SPIM)","volume":"31","author":"Engelbrecht","year":"2006","journal-title":"Optics Letters"},{"key":"bib6","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1364\/josaa.9.000154","type":"journal-article","article-title":"Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy","volume":"9","author":"Gibson","year":"1992","journal-title":"Journal of the Optical Society of America. A, Optics and Image Science"},{"key":"bib7","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1038\/nmeth.4218","type":"journal-article","article-title":"Adaptive optical fluorescence microscopy","volume":"14","author":"Ji","year":"2017","journal-title":"Nature Methods"},{"key":"bib8","doi-asserted-by":"publisher","first-page":"1585","DOI":"10.1038\/s41596-020-0313-9","type":"journal-article","article-title":"Tutorial: guidance for quantitative confocal microscopy","volume":"15","author":"Jonkman","year":"2020","journal-title":"Nature Protocols"},{"key":"bib9","doi-asserted-by":"publisher","first-page":"1067","DOI":"10.1038\/s43588-023-00568-2","type":"journal-article","article-title":"Spatial redundancy transformer for self-supervised fluorescence image denoising","volume":"3","author":"Li","year":"2023","journal-title":"Nature Computational Science"},{"key":"bib10","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adg9245","type":"journal-article","article-title":"Optimal sparsity allows reliable system-aware restoration of fluorescence microscopy images","volume":"9","author":"Mandracchia","year":"2023","journal-title":"Science Advances"},{"key":"bib11","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1007\/s12551-022-00949-3","type":"journal-article","article-title":"Deep learning-based image processing in optical microscopy","volume":"14","author":"Melanthota","year":"2022","journal-title":"Biophysical Reviews"},{"key":"bib12","doi-asserted-by":"publisher","first-page":"12905","DOI":"10.1364\/OE.24.012905","type":"journal-article","article-title":"Reducing effects of aberration in 3D fluorescence imaging using wavefront coding with a radially symmetric phase mask","volume":"24","author":"Patwary","year":"2016","journal-title":"Optics Express"},{"key":"bib13","doi-asserted-by":"publisher","first-page":"896","DOI":"10.1016\/j.cell.2014.10.010","type":"journal-article","article-title":"iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging","volume":"159","author":"Renier","year":"2014","journal-title":"Cell"},{"key":"bib14","doi-asserted-by":"publisher","first-page":"1396","DOI":"10.2174\/1570159X16666180302115544","type":"journal-article","article-title":"Cell death mechanisms in stroke and novel molecular and cellular treatment options","volume":"16","author":"Sekerdag","year":"2018","journal-title":"Current Neuropharmacology"},{"key":"bib15","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1007\/978-0-387-45524-2_23","type":"book-chapter","article-title":"Comparison of widefield\/deconvolution and confocal microscopy for three-dimensional imaging","volume-title":"Handbook Of Biological Confocal Microscopy","author":"Shaw","year":"2006"},{"key":"bib16","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1016\/j.cell.2014.03.042","type":"journal-article","article-title":"Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis","volume":"157","author":"Susaki","year":"2014","journal-title":"Cell"},{"key":"bib17","doi-asserted-by":"publisher","first-page":"1709","DOI":"10.1038\/nprot.2015.085","type":"journal-article","article-title":"Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging","volume":"10","author":"Susaki","year":"2015","journal-title":"Nature Protocols"},{"key":"bib18","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1038\/s41583-019-0250-1","type":"journal-article","article-title":"Tissue clearing and its applications in neuroscience","volume":"21","author":"Ueda","year":"2020","journal-title":"Nature Reviews. Neuroscience"},{"key":"bib19","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1038\/s41587-023-01717-8","type":"journal-article","article-title":"Reflective multi-immersion microscope objectives inspired by the Schmidt telescope","volume":"42","author":"Voigt","year":"2024","journal-title":"Nature Biotechnology"},{"key":"bib20","doi-asserted-by":"publisher","DOI":"10.1002\/advs.201903185","type":"journal-article","article-title":"MACS: rapid aqueous clearing system for 3D mapping of intact organs","volume":"7","author":"Zhu","year":"2020","journal-title":"Advanced Science"},{"key":"bib21","doi-asserted-by":"publisher","DOI":"10.1016\/j.crmeth.2023.100407","type":"journal-article","article-title":"A versatile vessel casting method for fine mapping of vascular networks using A hydrogel-based lipophilic dye solution","volume":"3","author":"Zhu","year":"2023","journal-title":"Cell Reports Methods"}],"container-title":["eLife"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdn.elifesciences.org\/articles\/101143\/elife-101143-v1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdn.elifesciences.org\/articles\/101143\/elife-101143-v1.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/elifesciences.org\/articles\/101143","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T09:48:19Z","timestamp":1787564899000},"score":1,"resource":{"primary":{"URL":"https:\/\/elifesciences.org\/articles\/101143"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,7]]},"references-count":21,"alternative-id":["10.7554\/eLife.101143"],"URL":"https:\/\/doi.org\/10.7554\/elife.101143","archive":["CLOCKSS"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.07.19.604108","asserted-by":"subject"},{"id-type":"doi","id":"10.1101\/2024.07.19.604108","asserted-by":"object"}],"is-same-as":[{"id-type":"doi","id":"10.7554\/eLife.101143.3","asserted-by":"subject"}],"is-version-of":[{"id-type":"doi","id":"10.7554\/eLife.101143.1","asserted-by":"subject"},{"id-type":"doi","id":"10.7554\/eLife.101143.2","asserted-by":"subject"}]},"ISSN":["2050-084X"],"issn-type":[{"value":"2050-084X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,7]]},"assertion":[{"value":"single anonymised","name":"peer_review_transparency","label":"Peer review transparency","group":{"name":"peer_review_taxonomy"}},{"value":"other reviewer(s), editor","name":"peer_review_interaction","label":"Peer review interaction","group":{"name":"peer_review_taxonomy"}},{"value":"review summaries, review reports, author\/editor communication, reviewer identities reviewer opt in, editor identities","name":"peer_review_published","label":"Peer review published","group":{"name":"peer_review_taxonomy"}},{"value":"open (sign in with ORCID iD required)","name":"post_publication_commenting","label":"Post publication commenting","group":{"name":"post_publication_commenting"}}],"article-number":"RP101143"}}