{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T13:34:46Z","timestamp":1793453686915,"version":"4.5.0"},"reference-count":40,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,10,9]],"date-time":"2021-10-09T00:00:00Z","timestamp":1633737600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017557","name":"Swiss National Centre of Competence in Research Kidney Control of Homeostasis","doi-asserted-by":"publisher","award":["153523"],"award-info":[{"award-number":["153523"]}],"id":[{"id":"10.13039\/501100017557","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017557","name":"Swiss National Centre of Competence in Research Kidney Control of Homeostasis","doi-asserted-by":"publisher","award":["185058"],"award-info":[{"award-number":["185058"]}],"id":[{"id":"10.13039\/501100017557","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"French National Research Agency","doi-asserted-by":"publisher","award":["ANR-11-EQPX-0031"],"award-info":[{"award-number":["ANR-11-EQPX-0031"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Neuroscience Methods"],"published-print":{"date-parts":[[2022,1]]},"DOI":"10.1016\/j.jneumeth.2021.109385","type":"journal-article","created":{"date-parts":[[2021,10,11]],"date-time":"2021-10-11T14:07:26Z","timestamp":1633961246000},"page":"109385","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":22,"special_numbering":"C","title":["Virtual histology of an entire mouse brain from formalin fixation to paraffin embedding. Part 2: Volumetric strain fields and local contrast changes"],"prefix":"10.1016","volume":"365","author":[{"given":"Griffin","family":"Rodgers","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine","family":"Tanner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Georg","family":"Schulz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra","family":"Migga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Willy","family":"Kuo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christos","family":"Bikis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mario","family":"Scheel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vartan","family":"Kurtcuoglu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timm","family":"Weitkamp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bert","family":"M\u00fcller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"5","key":"10.1016\/j.jneumeth.2021.109385_bib1","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1007\/s11307-018-1246-3","article-title":"X-ray-based 3D virtual histology-adding the next dimension to histological analysis","volume":"20","author":"Albers","year":"2018","journal-title":"Mol. Imaging Biol."},{"issue":"4","key":"10.1016\/j.jneumeth.2021.109385_bib2","doi-asserted-by":"crossref","first-page":"2221","DOI":"10.1002\/mrm.28543","article-title":"Myelin water imaging depends on white matter fiber orientation in the human brain","volume":"85","author":"Birkl","year":"2021","journal-title":"Magn. Reson. Med."},{"key":"10.1016\/j.jneumeth.2021.109385_bib3","doi-asserted-by":"crossref","unstructured":"C. Culling, Chapter 2: Methods of examination of tissues and cells, in: C. Culling (Ed.), Handbook of Histopathological and Histochemical Techniques, 3rd ed., Butterworth-Heinemann, 1974, 19\u201325.10.1016\/B978\u20130-407\u201372901-8.50009-3.","DOI":"10.1016\/B978-0-407-72901-8.50009-3"},{"issue":"6221","key":"10.1016\/j.jneumeth.2021.109385_bib4","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1126\/science.1260088","article-title":"Expansion microscopy","volume":"347","author":"Chen","year":"2015","journal-title":"Science"},{"issue":"3","key":"10.1016\/j.jneumeth.2021.109385_bib5","doi-asserted-by":"crossref","first-page":"1425","DOI":"10.1016\/j.neuroimage.2003.07.014","article-title":"Zen and the art of medical image registration: correspondence, homology, and quality","volume":"20","author":"Crum","year":"2003","journal-title":"NeuroImage"},{"issue":"3","key":"10.1016\/j.jneumeth.2021.109385_bib6","doi-asserted-by":"crossref","first-page":"297","DOI":"10.2307\/1932409","article-title":"Measures of the amount of ecologic association between species","volume":"26","author":"Dice","year":"1945","journal-title":"Ecology"},{"key":"10.1016\/j.jneumeth.2021.109385_bib7","doi-asserted-by":"crossref","DOI":"10.1523\/ENEURO.0195-17.2017","article-title":"Quantifying mesoscale neuroanatomy using X-ray microtomography","volume":"4","author":"Dyer","year":"2017","journal-title":"eNeuro"},{"key":"10.1016\/j.jneumeth.2021.109385_bib8","doi-asserted-by":"crossref","first-page":"136","DOI":"10.3389\/fnins.2020.00136","article-title":"The myelin water fraction serves as a marker for age-related myelin alterations in the cerebral white matter \u2013 a multiparametric MRI aging study","volume":"14","author":"Faizy","year":"2020","journal-title":"Front. Neurosci."},{"key":"10.1016\/j.jneumeth.2021.109385_bib9","doi-asserted-by":"crossref","DOI":"10.1016\/j.neuroimage.2021.118250","article-title":"Multi-modal imaging of a single mouse brain over five orders of magnitude of resolution","volume":"238","author":"Foxley","year":"2021","journal-title":"NeuroImage"},{"key":"10.1016\/j.jneumeth.2021.109385_bib10","doi-asserted-by":"crossref","DOI":"10.1016\/j.neuroimage.2019.116214","article-title":"Retrieving neuronal orientations using 3D scanning SAXS and comparison with diffusion MRI","volume":"204","author":"Georgiadis","year":"2020","journal-title":"NeuroImage"},{"issue":"1","key":"10.1016\/j.jneumeth.2021.109385_bib11","doi-asserted-by":"crossref","first-page":"2941","DOI":"10.1038\/s41467-021-22719-7","article-title":"Nanostructure-specific X-ray tomography reveals myelin levels, integrity and axon orientations in mouse and human nervous tissue","volume":"12","author":"Georgiadis","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jneumeth.2021.109385_bib12","series-title":"Computational Inverse Problems in Electrocardiology","first-page":"119","article-title":"The L-curve and its use in the numerical treatment of inverse problems","author":"Hansen","year":"2000"},{"issue":"2","key":"10.1016\/j.jneumeth.2021.109385_bib13","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1113\/jphysiol.1899.sp000755","article-title":"On the structure of cell protoplasm","volume":"24","author":"Hardy","year":"1899","journal-title":"J. Physiol."},{"key":"10.1016\/j.jneumeth.2021.109385_bib14","doi-asserted-by":"crossref","first-page":"32156","DOI":"10.1038\/srep32156","article-title":"Tomographic brain imaging with nucleolar detail and automatic cell counting","volume":"6","author":"Hieber","year":"2016","journal-title":"Sci. Rep."},{"issue":"8","key":"10.1016\/j.jneumeth.2021.109385_bib15","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1016\/j.ajpath.2019.05.004","article-title":"X-ray micro-computed tomography for nondestructive three-dimensional (3D) X-ray histology","volume":"189","author":"Katsamenis","year":"2019","journal-title":"Am. J. Pathol."},{"key":"10.1016\/j.jneumeth.2021.109385_bib16","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.neuroimage.2016.06.005","article-title":"Extending two-dimensional histology into the third dimension through conventional micro computed tomography","volume":"139","author":"Khimchenko","year":"2016","journal-title":"NeuroImage"},{"issue":"6","key":"10.1016\/j.jneumeth.2021.109385_bib17","article-title":"Hard X-ray nanoholotomography: large-scale, label-free, 3D neuroimaging beyond optical limit","volume":"5","author":"Khimchenko","year":"2018","journal-title":"Adv. Sci."},{"key":"10.1016\/j.jneumeth.2021.109385_bib18","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1109\/TMI.2009.2035616","article-title":"elastix: a toolbox for intensity-based medical image registration","volume":"29","author":"Klein","year":"2010","journal-title":"IEEE Trans. Med. Imag."},{"issue":"12","key":"10.1016\/j.jneumeth.2021.109385_bib19","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1038\/s41593-020-0704-9","article-title":"Dense neuronal reconstruction through X-ray holographic nano-tomography","volume":"23","author":"Kuan","year":"2020","journal-title":"Nat. Neurosci."},{"issue":"4","key":"10.1016\/j.jneumeth.2021.109385_bib20","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1177\/34.4.3081623","article-title":"Determination of lipid loss during aqueous and phase partition fixation using formalin and glutaraldehyde.","volume":"34","author":"Leist","year":"1986","journal-title":"J. Histochem. Cytochem."},{"key":"10.1016\/j.jneumeth.2021.109385_bib21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/neuro.05.001.2008","article-title":"In vivo 3D digital atlas database of the adult C57BL\/6J mouse brain by magnetic resonance microscopy","volume":"2","author":"Ma","year":"2008","journal-title":"Front. Neuroanat."},{"key":"10.1016\/j.jneumeth.2021.109385_bib22","series-title":"High-resolution tomographic imaging of microvessels","first-page":"89","author":"M\u00fcller","year":"2008"},{"key":"10.1016\/j.jneumeth.2021.109385_bib23","series-title":"2016 23rd International Conference on Pattern Recognition (ICPR)","first-page":"2294","article-title":"The truth is hard to make: validation of medical image registration","author":"Pluim","year":"2016"},{"issue":"4","key":"10.1016\/j.jneumeth.2021.109385_bib24","doi-asserted-by":"crossref","DOI":"10.3390\/cells9040812","article-title":"Myelin fat facts: an overview of lipids and fatty acid metabolism","volume":"9","author":"Poitelon","year":"2020","journal-title":"Cells"},{"issue":"1","key":"10.1016\/j.jneumeth.2021.109385_bib25","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/S0165-0270(97)00050-2","article-title":"The shrinkage of the human brain stem during formalin fixation and embedding in paraffin","volume":"75","author":"Quester","year":"1997","journal-title":"J. Neurosci. Methods"},{"key":"10.1016\/j.jneumeth.2021.109385_bib26","doi-asserted-by":"crossref","DOI":"10.1016\/j.jneumeth.2021.109354","article-title":"Virtual histology of an entire mouse brain from formalin fixation to paraffin embedding. Part 1: data acquisition, anatomical feature segmentation, global volume and density tracking","volume":"364","author":"Rodgers","year":"2021","journal-title":"J. Neurosci. Methods"},{"key":"10.1016\/j.jneumeth.2021.109385_bib27","series-title":"Non-rigid registration to determine strain fields during mouse brain fixation and embedding","first-page":"55","author":"Rodgers","year":"2021"},{"key":"10.1016\/j.jneumeth.2021.109385_bib28","unstructured":"Rodgers G., Schulz, G., Kuo, W., Tanner, C., M\u00fcller, B., Microtomography of a mouse brain from formalin fixed to paraffin embedded: datasets and registration parameters, 2021c. https:\/\/zenodo.org\/record\/4651412."},{"issue":"2","key":"10.1016\/j.jneumeth.2021.109385_bib29","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1109\/TMI.2002.808367","article-title":"Validation of nonrigid image registration using finite-element methods: application to breast MR images","volume":"22","author":"Schnabel","year":"2003","journal-title":"IEEE Trans. Med. Imag."},{"issue":"1","key":"10.1016\/j.jneumeth.2021.109385_bib30","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.jneumeth.2011.08.031","article-title":"Three-dimensional strain fields in human brain resulting from formalin fixation","volume":"202","author":"Schulz","year":"2011","journal-title":"J. Neurosci. Methods"},{"issue":"4","key":"10.1016\/j.jneumeth.2021.109385_bib31","first-page":"656","article-title":"Imaging the orientation of myelin sheaths in a non-stained histology slide of human brain","volume":"3","author":"Schulz","year":"2020","journal-title":"Prec. Nanomed."},{"key":"10.1016\/j.jneumeth.2021.109385_bib32","first-page":"50","article-title":"Fast parallel image registration on CPU and GPU for diagnostic classification of Alzheimer\u2019s disease","volume":"7","author":"Shamonin","year":"2014","journal-title":"Front. Neuroinform."},{"issue":"7","key":"10.1016\/j.jneumeth.2021.109385_bib33","doi-asserted-by":"crossref","first-page":"679","DOI":"10.3139\/146.111050","article-title":"Combined use of micro computed tomography and histology to evaluate the regenerative capacity of bone grafting materials","volume":"105","author":"Stalder","year":"2014","journal-title":"Int. J. Mater. Res."},{"key":"10.1016\/j.jneumeth.2021.109385_bib34","doi-asserted-by":"crossref","first-page":"12017","DOI":"10.1038\/s41598-018-30520-8","article-title":"Optimising complementary soft tissue synchrotron X-ray microtomography for reversibly-stained central nervous system samples","volume":"8","author":"Strotton","year":"2018","journal-title":"Sci. Rep."},{"issue":"27","key":"10.1016\/j.jneumeth.2021.109385_bib35","doi-asserted-by":"crossref","first-page":"6940","DOI":"10.1073\/pnas.1801678115","article-title":"Three-dimensional virtual histology of human cerebellum by X-ray phase-contrast tomography","volume":"115","author":"T\u00f6pperwien","year":"2018","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jneumeth.2021.109385_bib36","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/j.neuroimage.2019.05.043","article-title":"Contrast enhancement for visualizing neuronal cytoarchitecture by propagation-based X-ray phase-contrast tomography","volume":"199","author":"T\u00f6pperwien","year":"2019","journal-title":"NeuroImage"},{"key":"10.1016\/j.jneumeth.2021.109385_bib37","doi-asserted-by":"crossref","DOI":"10.1016\/j.neuroimage.2020.116523","article-title":"Correlative X-ray phase-contrast tomography and histology of human brain tissue affected by Alzheimer\u2019s disease","volume":"210","author":"T\u00f6pperwien","year":"2020","journal-title":"NeuroImage"},{"issue":"2","key":"10.1016\/j.jneumeth.2021.109385_bib38","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1002\/mrm.28776","article-title":"Synchrotron X-ray micro-CT as a validation dataset for diffusion MRI in whole mouse brain","volume":"86","author":"Trinkle","year":"2021","journal-title":"Magn. Reson. Med."},{"key":"10.1016\/j.jneumeth.2021.109385_bib39","first-page":"601","article-title":"Assessment of murine brain tissue shrinkage caused by different histological fixatives using magnetic resonance and computed tomography imaging","volume":"30","author":"Wehrl","year":"2015","journal-title":"Histol. Histopathol."},{"key":"10.1016\/j.jneumeth.2021.109385_bib40","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1016\/j.neuroimage.2006.01.015","article-title":"User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability","volume":"31","author":"Yushkevich","year":"2006","journal-title":"NeuroImage"}],"container-title":["Journal of Neuroscience Methods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0165027021003204?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0165027021003204?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,9,28]],"date-time":"2025-09-28T00:59:17Z","timestamp":1759021157000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0165027021003204"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1]]},"references-count":40,"alternative-id":["S0165027021003204"],"URL":"https:\/\/doi.org\/10.1016\/j.jneumeth.2021.109385","relation":{},"ISSN":["0165-0270"],"issn-type":[{"value":"0165-0270","type":"print"}],"subject":[],"published":{"date-parts":[[2022,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Virtual histology of an entire mouse brain from formalin fixation to paraffin embedding. Part 2: Volumetric strain fields and local contrast changes","name":"articletitle","label":"Article Title"},{"value":"Journal of Neuroscience Methods","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jneumeth.2021.109385","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 The Authors. Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"109385"}}