{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T13:20:24Z","timestamp":1773494424329,"version":"3.50.1"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,10,30]],"date-time":"2018-10-30T00:00:00Z","timestamp":1540857600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Med Imaging"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12880-018-0280-6","type":"journal-article","created":{"date-parts":[[2018,10,30]],"date-time":"2018-10-30T08:46:56Z","timestamp":1540889216000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["High-definition neural visualization of rodent brain using micro-CT scanning and non-local-means processing"],"prefix":"10.1186","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6650-1807","authenticated-orcid":false,"given":"Ko-Chin","family":"Chen","sequence":"first","affiliation":[]},{"given":"Alon","family":"Arad","sequence":"additional","affiliation":[]},{"given":"Zan-Ming","family":"Song","sequence":"additional","affiliation":[]},{"given":"David","family":"Croaker","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2018,10,30]]},"reference":[{"issue":"3","key":"280_CR1","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1007\/s00429-005-0073-x","volume":"211","author":"WJ Weninger","year":"2006","unstructured":"Weninger WJ, Geyer SH, Mohun TJ, Rasskin-Gutman D, Matsui T, Ribeiro I, et al. High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology. Anat Embryol. 2006;211(3):213\u201321.","journal-title":"Anat Embryol"},{"issue":"5567","key":"280_CR2","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1126\/science.1068206","volume":"296","author":"J Sharpe","year":"2002","unstructured":"Sharpe J, Ahlgren U, Perry P, Hill B, Ross A, Hecksher-S\u00f8rensen J, et al. Optical projection tomography as a tool for 3D microscopy and gene expression studies. Science. 2002;296(5567):541\u20135.","journal-title":"Science"},{"issue":"2","key":"280_CR3","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1006\/dbio.2001.0189","volume":"232","author":"M Dhenain","year":"2001","unstructured":"Dhenain M, Ruffins SW, Jacobs RE. Three-dimensional digital mouse atlas using high-resolution MRI. Dev Biol. 2001;232(2):458\u201370.","journal-title":"Dev Biol"},{"issue":"3","key":"280_CR4","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1002\/nbm.1146","volume":"20","author":"DH Turnbull","year":"2007","unstructured":"Turnbull DH, Mori S. MRI in mouse developmental biology. NMR Biomed. 2007;20(3):265\u201374.","journal-title":"NMR Biomed"},{"issue":"3","key":"280_CR5","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1002\/dvdy.21857","volume":"238","author":"BD Metscher","year":"2009","unstructured":"Metscher BD. MicroCT for developmental biology: a versatile tool for high-contrast 3D imaging at histological resolutions. Dev Dyn. 2009;238(3):632\u201340.","journal-title":"Dev Dyn"},{"issue":"13","key":"280_CR6","doi-asserted-by":"publisher","first-page":"2749","DOI":"10.1364\/AO.37.002749","volume":"37","author":"CL Smithpeter","year":"1998","unstructured":"Smithpeter CL, Dunn AK, Welch AJ, Richards-Kortum R. Penetration depth limits of in vivo confocal reflectance imaging. Appl Opt. 1998;37(13):2749\u201354.","journal-title":"Appl Opt"},{"issue":"4","key":"280_CR7","doi-asserted-by":"publisher","first-page":"282","DOI":"10.2174\/138920208784533601","volume":"9","author":"WJ Weninger","year":"2008","unstructured":"Weninger WJ, Geyer SH. Episcopic 3D imaging methods: tools for researching gene function. Curr Genomics. 2008;9(4):282\u20139.","journal-title":"Curr Genomics"},{"issue":"5","key":"280_CR8","doi-asserted-by":"publisher","first-page":"054070","DOI":"10.1117\/1.3000430","volume":"13","author":"T Alanentalo","year":"2008","unstructured":"Alanentalo T, Loren CE, Larefalk A, Sharpe J, Holmberg D, Ahlgren U. High-resolution three-dimensional imaging of islet-infiltrate interactions based on optical projection tomography assessments of the intact adult mouse pancreas. J Biomed Opt. 2008;13(5):054070.","journal-title":"J Biomed Opt"},{"key":"280_CR9","doi-asserted-by":"publisher","first-page":"592","DOI":"10.1100\/tsw.2007.125","volume":"7","author":"SW Ruffins","year":"2007","unstructured":"Ruffins SW, Martin M, Keough L, Truong S, Fraser SE, Jacobs RE, et al. Digital three-dimensional atlas of quail development using high-resolution MRI. TheScientificWorldJOURNAL. 2007;7:592\u2013604.","journal-title":"TheScientificWorldJOURNAL"},{"issue":"12","key":"280_CR10","doi-asserted-by":"publisher","first-page":"e84321","DOI":"10.1371\/journal.pone.0084321","volume":"8","author":"MD Wong","year":"2013","unstructured":"Wong MD, Spring S, Henkelman RM. Structural stabilization of tissue for embryo phenotyping using micro-CT with iodine staining. PLoS One. 2013;8(12):e84321.","journal-title":"PLoS One"},{"issue":"8","key":"280_CR11","doi-asserted-by":"publisher","first-page":"2179","DOI":"10.1007\/s11999-010-1766-x","volume":"469","author":"AJ Burghardt","year":"2011","unstructured":"Burghardt AJ, Link TM, Majumdar S. High-resolution computed tomography for clinical imaging of bone microarchitecture. Clin Orthop Relat Res. 2011;469(8):2179\u201393.","journal-title":"Clin Orthop Relat Res"},{"issue":"1","key":"280_CR12","doi-asserted-by":"publisher","first-page":"015011","DOI":"10.1088\/1748-6041\/3\/1\/015011","volume":"3","author":"ML Mather","year":"2008","unstructured":"Mather ML, Morgan SP, White LJ, Tai H, Kockenberger W, Howdle SM, et al. Image-based characterization of foamed polymeric tissue scaffolds. Biomed Mater. 2008;3(1):015011.","journal-title":"Biomed Mater"},{"issue":"4\u20135","key":"280_CR13","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1387\/ijdb.103229jm","volume":"55","author":"J Missbach-Guentner","year":"2011","unstructured":"Missbach-Guentner J, Hunia J, Alves F. Tumor blood vessel visualization. Int J Dev Biol. 2011;55(4\u20135):535\u201346.","journal-title":"Int J Dev Biol"},{"issue":"2","key":"280_CR14","doi-asserted-by":"publisher","first-page":"196","DOI":"10.4012\/dmj.2013-223","volume":"33","author":"S Nakagaki","year":"2014","unstructured":"Nakagaki S, Iijima M, Handa K, Koike T, Yasuda Y, Saito T, et al. Micro-CT and histologic analyses of bone surrounding immediately loaded miniscrew implants: comparing compression and tension loading. Dent Mater J. 2014;33(2):196\u2013202.","journal-title":"Dent Mater J"},{"issue":"6","key":"280_CR15","doi-asserted-by":"publisher","first-page":"2043","DOI":"10.1007\/s00198-011-1609-y","volume":"22","author":"F Peyrin","year":"2011","unstructured":"Peyrin F. Evaluation of bone scaffolds by micro-CT. Osteoporos int. 2011;22(6):2043\u20138.","journal-title":"Osteoporos int"},{"key":"280_CR16","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/1472-6793-9-11","volume":"9","author":"BD Metscher","year":"2009","unstructured":"Metscher BD. MicroCT for comparative morphology: simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues. BMC Physiol. 2009;9:11.","journal-title":"BMC Physiol"},{"issue":"1","key":"280_CR17","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1111\/jmi.12013","volume":"250","author":"E Pauwels","year":"2013","unstructured":"Pauwels E, Van Loo D, Cornillie P, Brabant L, Van Hoorebeke L. An exploratory study of contrast agents for soft tissue visualization by means of high resolution X-ray computed tomography imaging. J Microsc. 2013;250(1):21\u201331.","journal-title":"J Microsc"},{"key":"280_CR18","doi-asserted-by":"publisher","DOI":"10.1117\/12.935640","volume-title":"Developments in X-Ray Tomography Viii","author":"A Limaye","year":"2012","unstructured":"Limaye A. Drishti, A Volume Exploration and Presentation Tool. In: Developments in X-Ray Tomography Viii, vol. 8506; 2012."},{"issue":"7-8","key":"280_CR19","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1002\/mrd.22489","volume":"82","author":"Johannes Schindelin","year":"2015","unstructured":"Schindelin J, Rueden CT, Hiner MC, Eliceiri KW. The ImageJ ecosystem: An open platform for biomedical image analysis. Mol Reprod Dev. 2015;82(7-8):518\u201329.","journal-title":"Molecular Reproduction and Development"},{"key":"280_CR20","first-page":"502","volume-title":"Histological and histochemical methods : theory and practice","author":"JA Kiernan","year":"1999","unstructured":"Kiernan JA. Histological and histochemical methods : theory and practice. 3rd ed. Oxford: Butterworth-Heinemann; 1999. p. 502.","edition":"3"},{"key":"280_CR21","series-title":"2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR\u201905)","volume-title":"A non-local algorithm for image denoising","year":"2005","unstructured":"Buades A, Coll B, Morel JM, editors. A non-local algorithm for image denoising. 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR\u201905); 2005."},{"issue":"7","key":"280_CR22","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9(7):676\u201382.","journal-title":"Nat Methods"},{"issue":"4","key":"280_CR23","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1109\/TMI.2007.906087","volume":"27","author":"P Coup\u00e9","year":"2008","unstructured":"Coup\u00e9 P, Yger P, Prima S, Hellier P, Kervrann C, Barillot C. An optimized blockwise nonlocal means denoising filter for 3-D magnetic resonance images. IEEE Trans Med Imaging. 2008;27(4):425\u201341.","journal-title":"IEEE Trans Med Imaging"},{"issue":"1","key":"280_CR24","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/s13311-010-0002-4","volume":"8","author":"A Denic","year":"2011","unstructured":"Denic A, Macura SI, Mishra P, Gamez JD, Rodriguez M, Pirko I. MRI in rodent models of brain disorders. Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics. 2011;8(1):3\u201318.","journal-title":"Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics"},{"key":"280_CR25","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1016\/j.mri.2016.08.008","volume":"35","author":"R Gabbay-Benziv","year":"2017","unstructured":"Gabbay-Benziv R, Reece EA, Wang F, Bar-Shir A, Harman C, Turan OM, et al. A step-wise approach for analysis of the mouse embryonic heart using 17.6 tesla MRI. Magn Reson Imaging. 2017;35:46\u201353.","journal-title":"Magn Reson Imaging"},{"issue":"1","key":"280_CR26","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1016\/j.ymeth.2009.08.007","volume":"50","author":"SJ Schambach","year":"2010","unstructured":"Schambach SJ, Bag S, Schilling L, Groden C, Brockmann MA. Application of micro-CT in small animal imaging. Methods. 2010;50(1):2\u201313.","journal-title":"Methods"},{"key":"280_CR27","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1007\/978-1-59745-104-8_19","volume":"455","author":"M Stauber","year":"2008","unstructured":"Stauber M, Muller R. Micro-computed tomography: a method for the non-destructive evaluation of the three-dimensional structure of biological specimens. Methods Mol Biol. 2008;455:273\u201392.","journal-title":"Methods Mol Biol"},{"key":"280_CR28","doi-asserted-by":"publisher","first-page":"XIV, 486 S","DOI":"10.1017\/CBO9780511570216","volume-title":"Introduction to the blood-brain barrier methodology, biology, and pathology","author":"WM Pardridge","year":"1998","unstructured":"Pardridge WM. Introduction to the blood-brain barrier methodology, biology, and pathology. Cambridge: Cambridge University Press; 1998. p. XIV, 486 S."},{"issue":"1","key":"280_CR29","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1227\/01.NEU.0000097715.11966.8E","volume":"54","author":"EA Neuwelt","year":"2004","unstructured":"Neuwelt EA. Mechanisms of disease: the blood-brain barrier. Neurosurgery. 2004;54(1):131\u201340 discussion 41-2.","journal-title":"Neurosurgery"},{"key":"280_CR30","first-page":"xv, 1355","volume-title":"Advanced inorganic chemistry","author":"FA Cotton","year":"1999","unstructured":"Cotton FA, Cotton FA. Advanced inorganic chemistry. 6th ed. New York: Wiley; 1999. p. xv, 1355.","edition":"6"},{"issue":"1","key":"280_CR31","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1007\/BF01011535","volume":"6","author":"M Everett","year":"1974","unstructured":"Everett M, Miller W. The role of phosphotungstic and phosphomolybdic acids in connective tissue staining I. Histochemical studies. Histochem J. 1974;6(1):25\u201334.","journal-title":"Histochem J"},{"issue":"3","key":"280_CR32","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1002\/jez.b.22561","volume":"322","author":"PM Gignac","year":"2014","unstructured":"Gignac PM, Kley NJ. Iodine-enhanced micro-CT imaging: methodological refinements for the study of the soft-tissue anatomy of post-embryonic vertebrates. J Exp Zool B Mol Dev Evol. 2014;322(3):166\u201376.","journal-title":"J Exp Zool B Mol Dev Evol"},{"key":"280_CR33","first-page":"1","volume-title":"Structural inorganic chemistry","author":"AF Wells","year":"1984","unstructured":"Wells AF. Structural inorganic chemistry. 5th ed. Oxford: Clarendon Press; 1984. p. 1.","edition":"5"}],"container-title":["BMC Medical Imaging"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12880-018-0280-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12880-018-0280-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12880-018-0280-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,30]],"date-time":"2019-10-30T17:13:19Z","timestamp":1572455599000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcmedimaging.biomedcentral.com\/articles\/10.1186\/s12880-018-0280-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,10,30]]},"references-count":33,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["280"],"URL":"https:\/\/doi.org\/10.1186\/s12880-018-0280-6","relation":{},"ISSN":["1471-2342"],"issn-type":[{"value":"1471-2342","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,10,30]]},"assertion":[{"value":"20 November 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 October 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 October 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"All tissues and animals used in this study were handled with strict adherence to the requirements of the ACT Health Human Research Ethics Committee (ACTH-HREC) and Australian National University Animal Experimentation Ethics Committee (ANU-AEEC), project number A2011\/67.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"38"}}