{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T16:20:46Z","timestamp":1784046046974,"version":"3.55.0"},"reference-count":101,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2025,5,26]],"date-time":"2025-05-26T00:00:00Z","timestamp":1748217600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Banca del Monte di Lombardia Foundation, contribution to Prof. Roberto Pizzala, Dipartimento di Medicina Molecolare, University of Pavia 2021"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:sec>\n<jats:title>Background<\/jats:title>\n<jats:p>Volumetric atlases are an invaluable tool in neuroscience and otolaryngology, greatly aiding experiment planning and surgical interventions, as well as the interpretation of experimental and clinical data. The rat is a major animal model for hearing and balance studies, and a detailed volumetric atlas for the rat central auditory system (Waxholm) is available. However, the Waxholm rat atlas only contains a low-resolution inner ear featuring five structures. In the present work, we segmented and annotated 34 structures in the rat inner ear, yielding a detailed volumetric inner ear atlas which can be integrated with the Waxholm rat brain atlas.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Methods<\/jats:title>\n<jats:p>We performed iodine-enhanced microCT and iDISCO+-based clearing and fluorescence lightsheet microscopy imaging on a sample of rat temporal bones. Image stacks were segmented in a semiautomated way, and 34 inner ear volumes were reconstructed from five samples. Using geometrical morphometry, high-resolution segmentations obtained from lightsheet and microCT stacks were registered into the coordinate system of the Waxholm rat atlas.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>Cleared sample autofluorescence was used for the reconstruction of most inner ear structures, including fluid-filled compartments, nerves and sensory epithelia, blood vessels, and connective tissue structures. Image resolution allowed reconstruction of thin ducts (reuniting, saccular and endolymphatic), and the utriculoendolymphatic valve. The vestibulocochlear artery coursing through bone was found to be associated to the reuniting duct, and to be visible both in cleared and microCT samples, thus allowing to infer duct location from microCT scans. Cleared labyrinths showed minimal shape distortions, as shown by alignment with microCT and Waxholm labyrinths. However, membranous labyrinths could display variable collapse of the superior division, especially the roof of canal ampullae, whereas the inferior division (saccule and cochlea) was well preserved, with the exception of Reissner\u2019s membrane that could display ruptures in the second cochlear turn. As an example of atlas use, the volumes reconstructed from segmentations were used to separate macrophage populations from the spiral ganglion, auditory neuron dendrites, and Organ of Corti.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Conclusion<\/jats:title>\n<jats:p>We have reconstructed 34 structures from the rat temporal bone, which are available as both image stacks and printable 3D objects in a shared repository for download. These can be used for teaching, localizing cells or other features within the ear, modeling auditory and vestibular sensory physiology and training of automated segmentation machine learning tools.<\/jats:p>\n<\/jats:sec>","DOI":"10.7717\/peerj.19512","type":"journal-article","created":{"date-parts":[[2025,5,26]],"date-time":"2025-05-26T08:33:52Z","timestamp":1748248432000},"page":"e19512","source":"Crossref","is-referenced-by-count":5,"title":["Volumetric atlas of the rat inner ear from microCT and iDISCO+ cleared temporal bones"],"prefix":"10.7717","volume":"13","author":[{"given":"Daniele","family":"Cossellu","sequence":"first","affiliation":[{"name":"Department of Molecular Medicine, University of Pavia, Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisa","family":"Vivado","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, University of Pavia, Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Batti","sequence":"additional","affiliation":[{"name":"Wyss Center for Bio and Neuro Engineering, Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6351-8665","authenticated-orcid":true,"given":"Ivana","family":"Gantar","sequence":"additional","affiliation":[{"name":"Wyss Center for Bio and Neuro Engineering, Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4884-8265","authenticated-orcid":true,"given":"Roberto","family":"Pizzala","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, University of Pavia, Pavia, Italy"},{"name":"Fondazione IRCCS Policlinico San Matteo, Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5897-4444","authenticated-orcid":true,"given":"Paola","family":"Perin","sequence":"additional","affiliation":[{"name":"Fondazione IRCCS Policlinico San Matteo, Pavia, Italy"},{"name":"Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4443","published-online":{"date-parts":[[2025,5,26]]},"reference":[{"issue":"7767","key":"10.7717\/peerj.19512\/ref-1","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1038\/s41586-019-1419-5","article-title":"Meningeal lymphatic vessels at the skull base drain cerebrospinal fluid","volume":"572","author":"Ahn","year":"2019","journal-title":"Nature"},{"issue":"1","key":"10.7717\/peerj.19512\/ref-2","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/s1808-8694(15)30830-2","article-title":"Understanding the anatomy of ears from guinea pigs and rats and its use in basic otologic research","volume":"75","author":"Albuquerque","year":"2009","journal-title":"Brazilian Journal of Otorhinolaryngology"},{"key":"10.7717\/peerj.19512\/ref-3","doi-asserted-by":"publisher","first-page":"29","DOI":"10.3389\/fnagi.2014.00029","article-title":"Wistar rats: a forgotten model of age-related hearing loss","volume":"6","author":"Alvarado","year":"2014","journal-title":"Frontiers in Aging Neuroscience"},{"key":"10.7717\/peerj.19512\/ref-4","doi-asserted-by":"publisher","first-page":"1477282","DOI":"10.3389\/fneur.2024.1477282","article-title":"Is endolymphatic hydrops, as detected in MRI, a truly cochleocentric finding?","volume":"15","author":"\u00c1lvarez De Linera-Alperi","year":"2024","journal-title":"Frontiers in Neurology"},{"issue":"1\u20132","key":"10.7717\/peerj.19512\/ref-5","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1007\/BF00469735","article-title":"The influence of different fixatives and osmolality on the ultrastructure of the cochlear neuroepithelium","volume":"218","author":"Anniko","year":"1977","journal-title":"Archives of Oto-Rhino-Laryngology"},{"issue":"5","key":"10.7717\/peerj.19512\/ref-6","doi-asserted-by":"publisher","first-page":"105541","DOI":"10.1016\/j.nbd.2021.105541","article-title":"Auditory hypersensitivity and processing deficits in a rat model of fragile X syndrome","volume":"161","author":"Auerbach","year":"2021","journal-title":"Neurobiology of Disease"},{"issue":"1","key":"10.7717\/peerj.19512\/ref-7","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1007\/s11307-021-01657-2","article-title":"Side-by-side comparison of uPAR-targeting optical imaging antibodies and antibody fragments for fluorescence-guided surgery of solid tumors","volume":"25","author":"Baart","year":"2023","journal-title":"Molecular Imaging and Biology"},{"issue":"1","key":"10.7717\/peerj.19512\/ref-8","doi-asserted-by":"publisher","first-page":"16","DOI":"10.5935\/0946-5448.20130003","article-title":"Benign paroxysmal positional vertigo and tinnitus","volume":"18","author":"Barozzi","year":"2013","journal-title":"The International Tinnitus Journal"},{"key":"10.7717\/peerj.19512\/ref-9","doi-asserted-by":"publisher","DOI":"10.1002\/ar.1090680106","article-title":"The utriculo-endolymphatic valve and duct and its relation to the endolymphatic and saccular ducts in man and guinea pig. The Anatomical Record, 68, 1 and supplement no 1, 1937. 75-97","author":"Bast","year":"1937"},{"key":"10.7717\/peerj.19512\/ref-10","doi-asserted-by":"publisher","first-page":"17625","DOI":"10.1038\/s41598-019-53875-y","article-title":"Deconvolution of light sheet microscopy recordings","volume":"9","author":"Becker","year":"2019","journal-title":"Scientific Reports"},{"issue":"D1","key":"10.7717\/peerj.19512\/ref-11","doi-asserted-by":"publisher","first-page":"D981","DOI":"10.1093\/nar\/gkaa1083","article-title":"Mouse genome database (MGD): knowledgebase for mouse-human comparative biology","volume":"49","author":"Blake","year":"2021","journal-title":"Nucleic Acids Research"},{"issue":"8","key":"10.7717\/peerj.19512\/ref-12","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1369\/0022155419850099","article-title":"Tissue morphology and antigenicity in mouse and rat tibia: comparing 12 different decalcification conditions","volume":"67","author":"Bogoevski","year":"2019","journal-title":"Journal of Histochemistry & Cytochemistry"},{"issue":"2","key":"10.7717\/peerj.19512\/ref-13","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1016\/0378-5955(82)90069-7","article-title":"Auditory thresholds in rats of different age and strain. A behavioral and electrophysiological study","volume":"8","author":"Borg","year":"1982","journal-title":"Hearing Research"},{"key":"10.7717\/peerj.19512\/ref-14","doi-asserted-by":"publisher","first-page":"886","DOI":"10.1038\/s41467-017-00595-4","article-title":"A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction","volume":"8","author":"Bowl","year":"2017","journal-title":"Nature Communications"},{"issue":"1","key":"10.7717\/peerj.19512\/ref-15","doi-asserted-by":"publisher","first-page":"107956","DOI":"10.1016\/j.heares.2020.107956","article-title":"A new method for three-dimensional immunofluorescence study of the cochlea","volume":"392","author":"Brody","year":"2020","journal-title":"Hearing Research"},{"key":"10.7717\/peerj.19512\/ref-16","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1016\/j.heares.2016.06.007","article-title":"Endolymph movement visualized with light sheet fluorescence microscopy in an acute hydrops model","volume":"339","author":"Brown","year":"2016","journal-title":"Hearing Research"},{"key":"10.7717\/peerj.19512\/ref-17","doi-asserted-by":"publisher","first-page":"699674","DOI":"10.3389\/fneur.2021.699674","article-title":"Multimodal atlas of the murine inner ear: from embryo to adult","volume":"12","author":"Bryant","year":"2021","journal-title":"Frontiers in Neurology"},{"issue":"3","key":"10.7717\/peerj.19512\/ref-18","first-page":"207","article-title":"The mighty mouse: the impact of rodents on advances in biomedical research","volume":"110","author":"Bryda","year":"2013","journal-title":"Missouri Medicine"},{"issue":"7","key":"10.7717\/peerj.19512\/ref-19","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1016\/j.exger.2007.02.007","article-title":"Aging cochleas in the F344 rat: morphological and functional changes","volume":"42","author":"Buckiova","year":"2007","journal-title":"Experimental Gerontology"},{"issue":"3","key":"10.7717\/peerj.19512\/ref-20","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1002\/jmor.1051980303","article-title":"Cochlea in old world mice and rats (Muridae)","volume":"198","author":"Burda","year":"1988","journal-title":"Journal of Morphology"},{"issue":"5","key":"10.7717\/peerj.19512\/ref-21","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1369\/0022155413478613","article-title":"MicroCT versus sTSLIM 3D imaging of the mouse cochlea","volume":"61","author":"Buytaert","year":"2013","journal-title":"Journal of Histochemistry & Cytochemistry"},{"issue":"6","key":"10.7717\/peerj.19512\/ref-22","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1007\/s10162-011-0281-4","article-title":"Realistic 3D computer model of the gerbil middle ear, featuring accurate morphology of bone and soft tissue structures","volume":"12","author":"Buytaert","year":"2011","journal-title":"Journal of the Association for Research in Otolaryngology"},{"issue":"4","key":"10.7717\/peerj.19512\/ref-23","doi-asserted-by":"publisher","first-page":"1197","DOI":"10.1038\/s41596-022-00788-2","article-title":"Whole-mouse clearing and imaging at the cellular level with vDISCO","volume":"18","author":"Cai","year":"2023","journal-title":"Nature Protocols"},{"issue":"Pt 11","key":"10.7717\/peerj.19512\/ref-24","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/j.neurobiolaging.2017.09.034","article-title":"The FBN rat model of aging: investigation of ABR waveforms and ribbon synapse changes","volume":"62","author":"Cai","year":"2018","journal-title":"Neurobiology of Aging"},{"key":"10.7717\/peerj.19512\/ref-25","doi-asserted-by":"publisher","first-page":"108989","DOI":"10.1016\/j.heares.2024.108989","article-title":"The crucial role of diverse animal models to investigate cochlear aging and hearing loss","volume":"445","author":"Casta\u00f1o-Gonz\u00e1lez","year":"2024","journal-title":"Hearing Research"},{"issue":"5","key":"10.7717\/peerj.19512\/ref-26","doi-asserted-by":"publisher","first-page":"539","DOI":"10.3390\/bioengineering10050539","article-title":"Finite element modeling of residual hearing after cochlear implant surgery in chinchillas","volume":"10","author":"Castle","year":"2023","journal-title":"Bioengineering"},{"key":"10.7717\/peerj.19512\/ref-27","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-3195-9_14","article-title":"Image registration: fundamentals and recent advances based on deep learning","volume-title":"Machine Learning for Brain Disorders [Internet]","author":"Chen","year":"2023"},{"key":"10.7717\/peerj.19512\/ref-28","doi-asserted-by":"publisher","first-page":"615491","DOI":"10.3389\/fgene.2021.615491","article-title":"Advances in genome editing and application to the generation of genetically modified rat models","volume":"12","author":"Chenouard","year":"2021","journal-title":"Frontiers in Genetics"},{"issue":"1","key":"10.7717\/peerj.19512\/ref-29","doi-asserted-by":"publisher","first-page":"e17919","DOI":"10.7717\/peerj.17919","article-title":"Experimental assessment of diffusible iodine-based contrast-enhanced computed tomography (diceCT) protocols","volume":"12","author":"Costello","year":"2024","journal-title":"PeerJ"},{"issue":"1","key":"10.7717\/peerj.19512\/ref-30","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1097\/WCO.0000000000000770","article-title":"Physiology, clinical evidence and diagnostic relevance of sound-induced and vibration-induced vestibular stimulation","volume":"33","author":"Curthoys","year":"2020","journal-title":"Current Opinion in Neurology"},{"issue":"2","key":"10.7717\/peerj.19512\/ref-31","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1007\/BF00319118","article-title":"The endolymphatic duct and sac of the rat: a histological, ultrastructural, and immunocytochemical investigation","volume":"282","author":"Dahlmann","year":"1995","journal-title":"Cell and Tissue Research"},{"issue":"3","key":"10.7717\/peerj.19512\/ref-32","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1016\/S0194-5998(98)70052-X","article-title":"Hair cells in mammalian utricles","volume":"119","author":"Eatock","year":"1998","journal-title":"Otolaryngology\u2013Head and Neck Surgery"},{"issue":"6","key":"10.7717\/peerj.19512\/ref-33","doi-asserted-by":"publisher","first-page":"e66624","DOI":"10.1371\/journal.pone.0066624","article-title":"Comparative anatomy of the bony labyrinth (inner ear) of placental mammals","volume":"8","author":"Ekdale","year":"2013","journal-title":"PLOS ONE"},{"issue":"5","key":"10.7717\/peerj.19512\/ref-34","doi-asserted-by":"publisher","first-page":"3692","DOI":"10.1121\/1.5132553","article-title":"The rat animal model for noise-induced hearing loss","volume":"146","author":"Escabi","year":"2019","journal-title":"The Journal of the Acoustical Society of America"},{"key":"10.7717\/peerj.19512\/ref-35","first-page":"109","article-title":"The development of the central-peripheral transitional zone of the rat cochlear nerve. A light microscopic study","volume":"155","author":"Fraher","year":"1987","journal-title":"Journal of Anatomy"},{"key":"10.7717\/peerj.19512\/ref-36","doi-asserted-by":"publisher","DOI":"10.1101\/2024.02.21.581500","article-title":"Spiral ganglion neuron degeneration in deafened rats involves innate and adaptive immune responses not requiring complement","author":"Gansemer","year":"2024"},{"key":"10.7717\/peerj.19512\/ref-37","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1002\/(SICI)1097-0029(19970201)36:3<201::AID-JEMT8>3.0.CO;2-R","article-title":"Round window membrane. Structure function and permeability: a review","volume":"36","author":"Goycoolea","year":"1997","journal-title":"Microscopy Research and Technique"},{"key":"10.7717\/peerj.19512\/ref-38","doi-asserted-by":"crossref","DOI":"10.3109\/9780849375989","volume-title":"Anatomy of the temporal bone with surgical implications","author":"Gulya","year":"2007","edition":"3"},{"issue":"19","key":"10.7717\/peerj.19512\/ref-39","doi-asserted-by":"publisher","first-page":"2472","DOI":"10.1002\/1873-3468.14451","article-title":"A Hitchhiker\u2019s guide through the bio-image analysis software universe","volume":"596","author":"Haase","year":"2022","journal-title":"FEBS Letters"},{"issue":"2","key":"10.7717\/peerj.19512\/ref-40","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1111\/j.1365-2818.2009.03115.x","article-title":"Three-dimensional reconstruction of the guinea pig inner ear, comparison of OPFOS and light microscopy, applications of 3D reconstruction","volume":"233","author":"Hofman","year":"2009","journal-title":"Journal of Microscopy"},{"issue":"5","key":"10.7717\/peerj.19512\/ref-41","doi-asserted-by":"publisher","first-page":"3681","DOI":"10.1121\/1.5131344","article-title":"The rat as a model for studying noise injury and otoprotection","volume":"146","author":"Holt","year":"2019","journal-title":"The Journal of the Acoustical Society of America"},{"issue":"1\u20132","key":"10.7717\/peerj.19512\/ref-42","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3109\/00016488009127102","article-title":"The vascular anatomy of the rat cochlea","volume":"89","author":"Hornstrand","year":"1980","journal-title":"Acta Oto-Laryngologica"},{"issue":"11","key":"10.7717\/peerj.19512\/ref-43","doi-asserted-by":"publisher","first-page":"1491","DOI":"10.1177\/002215540305101109","article-title":"Network organization of interstitial connective tissue cells in the human endolymphatic duct","volume":"51","author":"Hultg\u00e5rd-Ekwall","year":"2003","journal-title":"Journal of Histochemistry & Cytochemistry"},{"issue":"4","key":"10.7717\/peerj.19512\/ref-44","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1002\/cne.24977","article-title":"Light sheet microscopy of the gerbil cochlea","volume":"529","author":"Hutson","year":"2021","journal-title":"Journal of Comparative Neurology"},{"key":"10.7717\/peerj.19512\/ref-45","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-1-60327-389-3_1","article-title":"The rat: a model used in biomedical research","volume-title":"Rat Genomics: Methods and Protocols Methods in Molecular Biology","author":"Jacob","year":"2010"},{"key":"10.7717\/peerj.19512\/ref-46","doi-asserted-by":"publisher","first-page":"173","DOI":"10.3389\/fnsys.2014.00173","article-title":"Mice and rats achieve similar levels of performance in an adaptive decision-making task","volume":"8","author":"Jaramillo","year":"2014","journal-title":"Frontiers in Systems Neuroscience"},{"issue":"2","key":"10.7717\/peerj.19512\/ref-47","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1007\/s12565-023-00755-1","article-title":"3D visualization and printing: an \u201cAnatomical Engineering\u201d trend revealing underlying morphology via innovation and reconstruction towards future of veterinary anatomy","volume":"99","author":"Kapoor","year":"2024","journal-title":"Anatomical Science International"},{"key":"10.7717\/peerj.19512\/ref-48","doi-asserted-by":"publisher","first-page":"108518","DOI":"10.1016\/j.heares.2022.108518","article-title":"Inner ear immunity","volume":"419","author":"Keithley","year":"2022","journal-title":"Hearing Research"},{"issue":"2","key":"10.7717\/peerj.19512\/ref-49","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1016\/0378-5955(92)90113-2","article-title":"Cochlear degeneration in aged rats of four strains","volume":"59","author":"Keithley","year":"1992","journal-title":"Hearing Research"},{"key":"10.7717\/peerj.19512\/ref-50","doi-asserted-by":"publisher","first-page":"83","DOI":"10.3389\/fnana.2018.00083","article-title":"Cell densities in the mouse brain: a systematic review","volume":"12","author":"Keller","year":"2018","journal-title":"Frontiers in Neuroanatomy"},{"issue":"18","key":"10.7717\/peerj.19512\/ref-51","doi-asserted-by":"publisher","first-page":"e2014472118","DOI":"10.1073\/pnas.2014472118","article-title":"Multiscale photonic imaging of the native and implanted cochlea","volume":"118","author":"Keppeler","year":"2021","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10.7717\/peerj.19512\/ref-52","first-page":"277","article-title":"3D slicer: a platform for subject-specific image analysis, visualization, and clinical support","volume-title":"Intraoperative Imaging Image-Guided Therapy","volume":"3(19)","author":"Kikinis","year":"2014"},{"key":"10.7717\/peerj.19512\/ref-53","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1016\/j.neuroimage.2014.12.080","article-title":"Waxholm Space atlas of the rat brain hippocampal region: three-dimensional delineations based on magnetic resonance and diffusion tensor imaging","volume":"108","author":"Kjonigsen","year":"2015","journal-title":"Neuroimage"},{"issue":"11","key":"10.7717\/peerj.19512\/ref-54","doi-asserted-by":"publisher","first-page":"1822","DOI":"10.1038\/s41592-023-02034-3","article-title":"Waxholm space atlas of the rat brain: a 3D atlas supporting data analysis and integration","volume":"20","author":"Kleven","year":"2023","journal-title":"Nature Methods"},{"issue":"1","key":"10.7717\/peerj.19512\/ref-55","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1007\/978-3-030-24281-7_6","article-title":"Applying geometric morphometrics to digital reconstruction and anatomical investigation","volume":"1171","author":"Landi","year":"2019","journal-title":"Advances in Experimental Medicine and Biology"},{"issue":"5","key":"10.7717\/peerj.19512\/ref-56","doi-asserted-by":"publisher","first-page":"1719","DOI":"10.1007\/s10439-010-9961-1","article-title":"Registration of micro-computed tomography and histological images of the guinea pig cochlea to construct an ear model using an iterative closest point algorithm","volume":"38","author":"Lee","year":"2010","journal-title":"Annals of Biomedical Engineering"},{"issue":"1","key":"10.7717\/peerj.19512\/ref-57","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1186\/s12915-022-01257-8","article-title":"Identification and characterisation of spontaneous mutations causing deafness from a targeted knockout programme","volume":"20","author":"Lewis","year":"2022","journal-title":"BMC Biology"},{"issue":"1","key":"10.7717\/peerj.19512\/ref-58","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1017\/s0022215100070018","article-title":"Regional differences in structure of the vestibular sensory regions","volume":"83","author":"Lindeman","year":"1969","journal-title":"The Journal of Laryngology & Otology"},{"issue":"1\u20132","key":"10.7717\/peerj.19512\/ref-59","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.heares.2008.05.009","article-title":"Three-dimensional imaging of the intact mouse cochlea by fluorescent laser scanning confocal microscopy","volume":"243","author":"MacDonald","year":"2008","journal-title":"Hearing Research"},{"key":"10.7717\/peerj.19512\/ref-60","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1016\/s0074-7742(03)56005-6","article-title":"The structure and physiology of the rat auditory system: an overview","volume":"56","author":"Malmierca","year":"2003","journal-title":"International Review of Neurobiology"},{"key":"10.7717\/peerj.19512\/ref-61","article-title":"The endolymphatic duct and sac of the rat\u2014a histophysiological study. Ph.D. Thesis, Radbound University, Nijmegen, the Netherlands","author":"Manni","year":"1987"},{"issue":"sup472","key":"10.7717\/peerj.19512\/ref-62","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3109\/00016489009121137","article-title":"The vascular anatomy of the vestibular labyrinth in man","volume":"472","author":"Mazzoni","year":"1990","journal-title":"Acta Oto-Laryngologica"},{"issue":"3","key":"10.7717\/peerj.19512\/ref-63","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1080\/03009734.2018.1492654","article-title":"Human inner ear blood supply revisited: the Uppsala collection of temporal bone-an international resource of education and collaboration","volume":"123","author":"Mei","year":"2018","journal-title":"Upsala Journal of Medical Sciences"},{"issue":"1","key":"10.7717\/peerj.19512\/ref-64","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/1472-6793-9-11","article-title":"MicroCT for comparative morphology: simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues","volume":"9","author":"Metscher","year":"2009","journal-title":"BMC Physiology"},{"key":"10.7717\/peerj.19512\/ref-65","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1016\/b978-012372560-8\/50021-8","article-title":"CHAPTER 21 - Non-parametric procedures","author":"Nichols","year":"2007","journal-title":"Statistical Parametric Mapping"},{"issue":"5","key":"10.7717\/peerj.19512\/ref-66","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1016\/j.neuroimage.2019.05.016","article-title":"Waxholm Space atlas of the rat brain auditory system: three-dimensional delineations based on structural and diffusion tensor magnetic resonance imaging","volume":"199","author":"Osen","year":"2019","journal-title":"Neuroimage"},{"key":"10.7717\/peerj.19512\/ref-67","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1016\/j.neuroimage.2014.04.001","article-title":"Waxholm space atlas of the sprague dawley rat brain","volume":"97","author":"Papp","year":"2014","journal-title":"Neuroimage"},{"key":"10.7717\/peerj.19512\/ref-68","doi-asserted-by":"publisher","first-page":"1386654","DOI":"10.3389\/fneur.2024.1386654","article-title":"Temporal bone marrow of the rat and its connections to the inner ear","volume":"15","author":"Perin","year":"2024","journal-title":"Frontiers in Neurology"},{"key":"10.7717\/peerj.19512\/ref-69","doi-asserted-by":"publisher","first-page":"2017","DOI":"10.3389\/fnana.2019.00015","article-title":"IDISCO+ for the study of neuroimmune architecture of the rat auditory brainstem","volume":"13","author":"Perin","year":"2019","journal-title":"Frontiers in Neuroanatomy"},{"issue":"11","key":"10.7717\/peerj.19512\/ref-70","doi-asserted-by":"publisher","first-page":"2129","DOI":"10.1111\/2041-210X.13689","article-title":"ALPACA: a fast and accurate computer vision approach for automated landmarking of three-dimensional biological structures","volume":"12","author":"Porto","year":"2021","journal-title":"Methods in Ecology and Evolution"},{"issue":"5\u20136","key":"10.7717\/peerj.19512\/ref-71","doi-asserted-by":"publisher","first-page":"315","DOI":"10.3109\/00016487909137175","article-title":"The vascular supply of the endolymphatic sac","volume":"88","author":"Rask-Andersen","year":"1979","journal-title":"Acta Oto-Laryngologica"},{"issue":"6982","key":"10.7717\/peerj.19512\/ref-72","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/nature02426","article-title":"Genome sequence of the Brown Norway rat yields insights into mammalian evolution","volume":"428","author":"Gibbs","year":"2004","journal-title":"Nature"},{"issue":"4","key":"10.7717\/peerj.19512\/ref-73","doi-asserted-by":"publisher","first-page":"896","DOI":"10.1016\/j.cell.2014.10.010","article-title":"Resource iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging","volume":"159","author":"Renier","year":"2014","journal-title":"Cell"},{"issue":"4","key":"10.7717\/peerj.19512\/ref-74","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1016\/j.anorl.2017.01.001","article-title":"Imaging and cell count in cleared intact cochlea in the Mongolian gerbil using laser scanning confocal microscopy","volume":"134","author":"Risoud","year":"2017","journal-title":"European Annals of Otorhinolaryngology, Head and Neck Diseases"},{"key":"10.7717\/peerj.19512\/ref-75","doi-asserted-by":"publisher","DOI":"10.1111\/2041-210X.13669","article-title":"SlicerMorph: an open and extensible platform to retrieve, visualize and analyze 3D morphology","author":"Rolfe","year":"2020"},{"issue":"2","key":"10.7717\/peerj.19512\/ref-76","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1369\/0022155410394857","article-title":"Light sheet fluorescence microscopy: a review","volume":"59","author":"Santi","year":"2011","journal-title":"The Journal of Histochemistry and Cytochemistry"},{"issue":"1\u20132","key":"10.7717\/peerj.19512\/ref-77","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/j.heares.2004.01.017","article-title":"The digital cytocochleogram","volume":"192","author":"Santi","year":"2004","journal-title":"Hearing Research"},{"issue":"187","key":"10.7717\/peerj.19512\/ref-78","doi-asserted-by":"publisher","first-page":"e64420","DOI":"10.3791\/64420","article-title":"Imaging the aging cochlea with light-sheet fluorescence microscopy","author":"Santi","year":"2022","journal-title":"Journal of Visualized Experiments"},{"issue":"7","key":"10.7717\/peerj.19512\/ref-79","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nature Methods"},{"issue":"1","key":"10.7717\/peerj.19512\/ref-80","doi-asserted-by":"publisher","first-page":"4840","DOI":"10.1038\/s41598-023-31235-1","article-title":"First evidence of the link between internal and external structure of the human inner ear otolith system using 3D morphometric modeling","volume":"13","author":"Smith","year":"2023","journal-title":"Scientific Reports"},{"key":"10.7717\/peerj.19512\/ref-81","doi-asserted-by":"publisher","DOI":"10.1002\/ar.25534","article-title":"A morphometric comparison of the ductus reuniens in humans and guinea pigs, with a note on its evolutionary importance","author":"Smith","year":"2024","journal-title":"The Anatomical Record"},{"issue":"5","key":"10.7717\/peerj.19512\/ref-82","doi-asserted-by":"publisher","first-page":"1037","DOI":"10.1002\/ar.24675","article-title":"Three-dimensional visualization of the human membranous labyrinth: the membrana limitans and its role in vestibular form","volume":"305","author":"Smith","year":"2022a","journal-title":"The Anatomical Record"},{"issue":"5","key":"10.7717\/peerj.19512\/ref-83","doi-asserted-by":"publisher","first-page":"633","DOI":"10.1007\/s10162-022-00858-y","article-title":"Insights into inner ear function and disease through novel visualization of the ductus reuniens, a seminal communication between hearing and balance mechanisms","volume":"23","author":"Smith","year":"2022b","journal-title":"Journal of the Association for Research in Otolaryngology"},{"issue":"8","key":"10.7717\/peerj.19512\/ref-84","doi-asserted-by":"publisher","first-page":"3706","DOI":"10.1523\/JNEUROSCI.4067-12.2013","article-title":"Tuning and timing in mammalian type I hair cells and calyceal synapses","volume":"33","author":"Songer","year":"2013","journal-title":"The Journal of Neuroscience"},{"key":"10.7717\/peerj.19512\/ref-85","volume-title":"\u00dcber das Durchsichtigmachen von Menschlichen und Tierischen Pr\u00e4paraten","author":"Spalteholz","year":"1911"},{"issue":"S1","key":"10.7717\/peerj.19512\/ref-86","doi-asserted-by":"publisher","first-page":"S10","DOI":"10.1007\/s00415-015-7909-y","article-title":"Vestibular animal models: contributions to understanding physiology and disease","volume":"1","author":"Straka","year":"2016","journal-title":"Journal of Neurology"},{"issue":"4","key":"10.7717\/peerj.19512\/ref-87","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1162\/qss_a_00277","article-title":"Disappearing repositories: taking an infrastructure perspective on the long-term availability of research data","volume":"4","author":"Strecker","year":"2023","journal-title":"Quantitative Science Studies"},{"issue":"3","key":"10.7717\/peerj.19512\/ref-88","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1016\/j.neuron.2020.03.004","article-title":"Whole-brain profiling of cells and circuits in mammals by tissue clearing and light-sheet microscopy","volume":"106","author":"Ueda","year":"2020","journal-title":"Neuron"},{"issue":"2","key":"10.7717\/peerj.19512\/ref-89","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1038\/s41583-019-0250-1","article-title":"Tissue clearing and its applications in neuroscience","volume":"21","author":"Ueda","year":"2020","journal-title":"Nature Reviews Neuroscience"},{"issue":"4","key":"10.7717\/peerj.19512\/ref-90","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1016\/j.media.2016.06.011","article-title":"Open-source platforms for navigated image-guided interventions","volume":"33","author":"Ungi","year":"2016","journal-title":"Medical Image Analysis"},{"issue":"3","key":"10.7717\/peerj.19512\/ref-91","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1007\/s12565-023-00703-z","article-title":"Three-dimensional mouse cochlea imaging based on the modified Sca\/eS using confocal microscopy","volume":"98","author":"Urata","year":"2023","journal-title":"Anatomical Science International"},{"issue":"1\u20132","key":"10.7717\/peerj.19512\/ref-92","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/j.heares.2007.07.008","article-title":"Attachment of the utricular and saccular maculae to the temporal bone","volume":"233","author":"Uzun-Coruhlu","year":"2007","journal-title":"Hearing Research"},{"key":"10.7717\/peerj.19512\/ref-93","doi-asserted-by":"publisher","first-page":"103720","DOI":"10.1016\/j.mcn.2022.103720","article-title":"Methods for multiscale structural and functional analysis of the mammalian cochlea","volume":"120","author":"Vogl","year":"2022","journal-title":"Molecular and Cellular Neuroscience"},{"issue":"11","key":"10.7717\/peerj.19512\/ref-94","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1038\/s41592-019-0554-0","article-title":"The MesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue","volume":"16","author":"Voigt","year":"2019","journal-title":"Nature Methods"},{"issue":"6","key":"10.7717\/peerj.19512\/ref-95","doi-asserted-by":"publisher","first-page":"a033555","DOI":"10.1101\/cshperspect.a033555","article-title":"Interactions between macrophages and the sensory cells of the inner ear","volume":"9","author":"Warchol","year":"2019","journal-title":"Cold Spring Harbor Perspectives in Medicine"},{"issue":"6","key":"10.7717\/peerj.19512\/ref-96","doi-asserted-by":"publisher","first-page":"2732","DOI":"10.1038\/s41596-021-00502-8","article-title":"Tutorial: practical considerations for tissue clearing and imaging","volume":"16","author":"Weiss","year":"2021","journal-title":"Nature Protocols"},{"issue":"1","key":"10.7717\/peerj.19512\/ref-97","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1016\/j.imbio.2018.09.002","article-title":"Are rats more human than mice?","volume":"224","author":"Wildner","year":"2019","journal-title":"Immunobiology"},{"issue":"2","key":"10.7717\/peerj.19512\/ref-98","doi-asserted-by":"publisher","first-page":"1684","DOI":"10.1152\/jn.00649.2006","article-title":"Developmental changes in two voltage-dependent sodium currents in utricular hair cells","volume":"97","author":"Wooltorton","year":"2007","journal-title":"Journal of Neurophysiology"},{"issue":"5\u20136","key":"10.7717\/peerj.19512\/ref-99","doi-asserted-by":"publisher","first-page":"352","DOI":"10.3109\/00016487709123977","article-title":"Responses of squirrel monkey vestibular neurons to audio-frequency sound and head vibration","volume":"84","author":"Young","year":"1977","journal-title":"Acta Oto-Laryngologica"},{"key":"10.7717\/peerj.19512\/ref-100","doi-asserted-by":"publisher","first-page":"3342","DOI":"10.1109\/EMBC.2016.7591443","article-title":"ITK-SNAP: an interactive tool for semi-automatic segmentation of multi-modality biomedical images","volume":"2016","author":"Yushkevich","year":"2016","journal-title":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)"},{"issue":"3","key":"10.7717\/peerj.19512\/ref-101","doi-asserted-by":"publisher","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":["PeerJ"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/peerj.com\/articles\/19512.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/19512.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/19512.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/19512.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,26]],"date-time":"2025-05-26T08:33:59Z","timestamp":1748248439000},"score":1,"resource":{"primary":{"URL":"https:\/\/peerj.com\/articles\/19512"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,26]]},"references-count":101,"alternative-id":["10.7717\/peerj.19512"],"URL":"https:\/\/doi.org\/10.7717\/peerj.19512","archive":["CLOCKSS","LOCKSS","Portico"],"relation":{},"ISSN":["2167-8359"],"issn-type":[{"value":"2167-8359","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,26]]},"article-number":"e19512"}}