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190 results for “Inner ear”
Zellige example dataset: inner ear organoid epithelium
<p><strong>Inner ear organoid at day 14 of culture. </strong></p> <p>The z-stack image encompasses half of the spherical organoid including two distinct and superimposed surfaces that correspond to the basal side of the epithelium and the apical junctional network. It was acquired with a confocal microscope (Nikon A1HD25) equipped with a Nikon Plan-Apochromat 25x lens (NA=1.05). Pixel size 0.690 µm, z step >1 µm. This dataset contains both the ground-truth height maps and the height maps generated with Zellige. The Zellige parameters used are:</p> <p><span class="math-tex">\(T_{A}=5, T_{otsu}=12, S_{min}=5, \sigma_{xy}=2, \sigma_{z}=1, T_{OSE1}=0.9, R_{1}=5, C_{1}=0.8, T_{OSE2}=0.1, R_{2}=10, C_{2}=0.8.\)</span></p> <p>Nota: to compare the ground truth height map with the Zellige height map, one first needs to substrat 1 to all values of the Zellige height map.</p> <p>See the accompanying paper: Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool. Trébeau <em>et al.</em> 2022: <a href="https://doi.org/10.1101/2022.04.05.485876">https://doi.org/10.1101/2022.04.05.485876</a></p>
Influence of the cochlear partition's flexibility on the macro mechanisms in the inner ear
<p>This repository contains the research data for the article Kersten, S., Taschke, H., & Vorländer, M. (2024). Influence of the cochlear partition’s flexibility on the macro mechanisms in the inner ear. Hearing Research, 109127. <a href="https://doi.org/10.1016/j.heares.2024.109127">https://doi.org/10.1016/j.heares.2024.109127</a>.</p> <p>It includes a finite element model of the inner ear, simulation results, and a Python script with code used for the analysis.</p> <div> <h2>Abstract</h2> <div> <div>Recent studies have highlighted the anatomy of the cochlear partition (CP), revealing insights into the flexible nature of the osseous spiral lamina (OSL) and the existence of a flexible cochlear partition bridge (CPB) between the OSL and the basilar membrane (BM). However, most existing inner ear models treat the OSL as a rigid structure and ignore the CPB, neglecting their potential impact on intracochlear sound pressure and motion of the BM. In this paper, we investigate the effect of the CP’s flexibility by including the OSL and CPB as either rigid or flexible structures in a numerical anatomical model of the human inner ear. Our findings demonstrate that the flexibility of the OSL and the presence of the CPB significantly affect cochlear macro mechanisms, including differential intracochlear sound pressure, resistive behavior in cochlear impedances, CP stiffness, and BM velocity. These results emphasize the importance of considering the flexibility of the entire CP to enhance our understanding of cochlear function and to accurately interpret experimental data on inner ear mechanics.</div> </div> </div>
Human Inner Ear Anatomy: Labeled Volume CT Data of Inner Ear Fluid Space and Anatomical Landmarks
<p>The provided dataset comprises 43 instances of temporal bone volume CT scans. The scans were performed on human cadaveric specimen with a resulting isotropic voxel size of <span class="math-tex">\(99 \times 99 \times 99 \, \, \mathrm{\mu m}^3\)</span>. Voxel-wise image labels of the fluid space of the bony labyrinth, subdivided in the three semantic classes cochlear volume, vestibular volume and semicircular canal volume are provided. In addition, each dataset contains JSON-like descriptor data defining the voxel coordinates of the anatomical landmarks: (1) apex of the cochlea, (2) oval window and (3) round window. The dataset can be used to train and evaluate algorithmic machine learning models for automated innear ear analysis in the context of the supervised learning paradigm.</p> <p> </p> <p><strong>Usage Notes</strong></p> <p>The datasets are formatted in the HDF5 format developed by the <a href="https://www.hdfgroup.org/solutions/hdf5/">HDF5 Group</a>. We utilized and thus recommend the usage of Python bindings <a href="https://www.h5py.org/">pyHDF</a> to handle the datasets.</p> <p>The flat-panel volume CT raw data, labels and landmarks are saved in the HDF5-internal file structure using the respective group and datasets:</p> <pre><code>raw/raw-0 label/label-0 landmark/landmark-0 landmark/landmark-1 landmark/landmark-2</code></pre> <p>Array raw and label data can be read from the file by indexing into an opened h5py file handle, for example as numpy.ndarray. Further metadata is contained in the attribute dictionaries of the raw and label datasets.</p> <p>Landmark coordinate data is available as an attribute dict and contains the coordinate system (LPS or RAS), IJK voxel coordinates and label information. The helicotrema or cochlea top is globally saved in landmark 0, the oval window in landmark 1 and the round window in landmark 2. Read as a Python dictionary, exemplary landmark information for a dataset may reads as follows:</p> <pre><code class="language-python">{'coordsys': 'LPS', 'id': 1, 'ijk_position': array([181, 188, 100]), 'label': 'CochleaTop', 'orientation': array([-1., -0., -0., -0., -1., -0., 0., 0., 1.]), 'xyz_position': array([ 44.21109689, -139.38058589, -183.48249736])}</code></pre> <p> </p> <pre><code class="language-python">{'coordsys': 'LPS', 'id': 2, 'ijk_position': array([222, 182, 145]), 'label': 'OvalWindow', 'orientation': array([-1., -0., -0., -0., -1., -0., 0., 0., 1.]), 'xyz_position': array([ 48.27890112, -139.95991131, -179.04103763])}</code></pre> <p> </p> <pre><code class="language-python">{'coordsys': 'LPS', 'id': 3, 'ijk_position': array([223, 209, 147]), 'label': 'RoundWindow', 'orientation': array([-1., -0., -0., -0., -1., -0., 0., 0., 1.]), 'xyz_position': array([ 48.33120126, -137.27135678, -178.8665465 ])}</code></pre> <p> </p>
Supplementary material for "The inner ear anatomy of glyptodonts and pampatheres (Xenarthra, Cingulata): functional and phylogenetic implications"
<p><strong>Left_inner_ear_Doedicurus.stl</strong>: digital model of the inner ear of <em>Doedicurus </em>in stl format.</p> <p><strong>Left_inner_ear_Glyptodon.stl</strong>: digital model of the inner ear of <em>Glyptodon </em>in stl format.</p> <p><strong>Left_inner_ear_Holmesina.stl</strong>: digital model of the inner ear of <em>Holmesina</em> in stl format.</p> <p><strong>Left_inner_ear_Panochthus.stl</strong>: digital model of the inner ear of <em>Panochthus </em>in stl format.</p> <p><strong>Left_inner_ear_Pseudoplohophorus.stl</strong>: digital model of the inner ear of <em>Pseudoplohophorus </em>in stl format.</p> <p><strong>Matrix.nex:</strong> Matrix used to perform the phylogenetic analysis of xenarthrans based on inner ear characters.</p> <p><strong>PC1, PC2, PC3 loadings plot.pdf:</strong> Figures showing the loadings of the morphometric variables in each of the first three principal components.</p> <p><strong>Principal Components Analysis.xlsx:</strong> Spreadsheet with the results of the Principal Components Analysis: PC summary, PC scores, and PC loadings.</p> <p>T<strong>able S1. Deviation from orthogonality.pdf:</strong> Deviation from orthogonality (log<sub>10</sub>90var), and agility categories from Spoor et al. (2007).</p> <p><strong>Tree-PGLS.tre:</strong> Tree based on the most recent phylogenetic hypotheses using molecular and morphological data and time-scaled a posteriori, to perform the PGLS analysis with the morphological data of the inner ear.</p> <p> </p>
Fig. 2 in The endocranial morphology and inner ear of the abelisaurid theropod Aucasaurus garridoi
Fig. 2. Abelisaurid theropod Aucasaurus garridoi Coria, Chiappe, and Dingus, 2002, from the Upper Cretaceous of North Patagonia (MCF-PVPH 236). Digital reconstruction of the right inner ear in lateral (A), dorsal (B), anterior (C), and posterior (D) views.
Fig. 1 in The endocranial morphology and inner ear of the abelisaurid theropod Aucasaurus garridoi
Fig. 1. Abelisaurid theropod Aucasaurus garridoi Coria, Chiappe, and Dingus, 2002 (MCF-PVPH 236), from the Upper Cretaceous of North Patagonia, in dorsal (A) and right lateral (B) views. Volume rendering of the braincase (semi-transparent) and cranial endocast (A 1, B1), and line drawings of brain and inner ear (A 2, B2).
Data from: Non-invasive biophysical measurement of travelling waves in the insect inner ear
Frequency analysis in the mammalian cochlea depends on the propagation of frequency information in the form of a travelling wave (TW) across tonotopically arranged auditory sensilla. TWs have been directly observed in the basilar papilla of birds and the ears of bush-crickets (Insecta: Orthoptera) and have also been indirectly inferred in the hearing organs of some reptiles and frogs. Existing experimental approaches to measure TW function in tetrapods and bush-crickets are inherently invasive, compromising the fine-scale mechanics of each system. Located in the forelegs, the bush-cricket ear exhibits outer, middle and inner components; the inner ear containing tonotopically arranged auditory sensilla within a fluid-filled cavity, and externally protected by the leg cuticle. Here, we report bush-crickets with transparent ear cuticles as potential model species for direct, non-invasive measuring of TWs and tonotopy. Using laser Doppler vibrometry and spectroscopy, we show that increased transmittance of light through the ear cuticle allows for effective non-invasive measurements of TWs and frequency mapping. More transparent cuticles allow several properties of TWs to be precisely recovered and measured in vivo from intact specimens. Our approach provides an innovative, non-invasive alternative to measure the natural motion of the sensilla-bearing surface embedded in the intact inner ear fluid.
Data from: Intraspecific variation and symmetry of the inner-ear labyrinth in a population of wild turkeys: implications for paleontological reconstructions
The cochlea and semicircular canals of the inner ear are vital neurosensory devices. There are associations between the anatomy of these sensorineural structures, their function, and the function of related biological systems, e.g., hearing ability, gaze stabilization, locomotor agility, and posture. The endosseous labyrinth is frequently used as a proxy to infer the performance of the hearing and vestibular systems, locomotor abilities, and ecology of extinct species. Such fossil inferences are often based on single specimens or even a single ear, representing an entire species. To address whether a single ear is representative of a population, we used geometric morphometrics to quantitatively assess the variation in shape and symmetry in a sample of endosseous labyrinths of wild turkeys Meleagris gallopavo of southern Ohio. We predicted that ears would be symmetrical both within individuals and across the sample; that labyrinth shape and size would covary; that labyrinth shape would vary with the size of the brain, measured as width of the endocranium at the cerebellum; and that labyrinths would be morphologically integrated. To test these predictions, we microCT-scanned the heads of 26 cadaveric turkeys, digitally segmented their endosseous labyrinths in Avizo, and assigned 15 manual landmarks and 20 sliding semilandmarks to each digital model. Following Procrustes alignment, we conducted an analysis of bilateral symmetry, a Procrustes regression analysis for allometry and other covariates including side and replicate, and analyses of global integration and modularity. Based on Procrustes distances, no individual's left and right ears were clearly different from each other. When comparing the ears of different specimens, statistically clear differences in shape were found in only 66 of more than 1300 contrasts. Moreover, effects of both directional and fluctuating asymmetry were very small—generally, two orders of magnitude smaller than the variance explained by individual variation. Statistical tests disagreed on whether these asymmetric effects crossed the threshold of significance, possibly due to non-isotropic variation among landmarks. Regardless, labyrinths appeared to primarily vary in shape symmetrically. Neither labyrinth size nor endocranial width was correlated with labyrinth shape, contrary to our expectations. Finally, labyrinths were found to be moderately integrated in a global sense, but four weakly separated modules—the three semicircular canals and cochlea—were recovered using a maximum-likelihood analysis. The results show that both fluctuating and directional asymmetry play a larger role in shape variation than expected—but nonetheless, endosseous labyrinths are symmetrical within individuals and at the level of the population, and their shape varies symmetrically. Thus, inferences about populations, and very possibly species, may be confidently made when only a single specimen, or even a single ear, is available for study.
Quantification of hair cell number, ribeye b and nuclei in the zebrafish inner ear endorgans
<p>The three otolithic endorgans of the inner ear are known to be involved in sound detection in different teleost fishes, yet their relative roles for auditory-vestibular functions within the same species remain unclear. In zebrafish (<em>Danio</em> <em>rerio</em>), saccule and utricle are thought to play key functions in encoding auditory and vestibular information, respectively, but the biological function of the lagena is not clear. We hypothesized that the zebrafish saccule serves as a <span>primary </span>auditory endorgan, <span>making it more vulnerable to noise exposure</span>, and that lagena might have an auditory function given its connectivity to the saccule and dominant vestibular function of the utricle.</p> <p>In this study, we compared the impact of acoustic trauma (continuous white noise at 168 dB for 24 h) between the sensory epithelia of the three otolithic endorgans. Noise treatment caused hair cell loss in both the saccule and lagena but not in the utricle. This effect was identified immediately after acoustic treatment and did not increase 24 h post trauma. Furthermore, hair cell loss was accompanied by a reduction in presynaptic activity measured based on Ribeye b presence but mainly in the saccule, supporting its main contribution for noise-induced hearing loss.</p> <p>Our findings support the hypothesis that the saccule plays a major role in sound detection and that lagena is also acoustically affected extending the species hearing dynamic range.</p>
Magnetic Resonance Imaging Evaluation of Inner Ear Pathology Using Intra-Tympanic Contrast Agent
ClinicalTrials.gov study NCT02080312. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A Clinical Trial of Anakinra for Steroid-Resistant Autoimmune Inner Ear Disease
ClinicalTrials.gov study NCT01267994. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Variation and disparity within the inner ear and trigeminus of the Tenrecomorpha
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AAV-mediated Inner ear gene delivery triggers mild host immune responses in the mammalian inner ear
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Data from: Intraspecific variation and symmetry of the inner-ear labyrinth in a population of wild turkeys: implications for paleontological reconstructions
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Quantification of hair cell number, ribeye b and nuclei in the zebrafish inner ear endorgans
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Data from: Non-invasive biophysical measurement of travelling waves in the insect inner ear
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Data from: Inner ear morphology of diadectomorphs and seymouriamorphs (Tetrapoda) uncovered by high-resolution x-ray microcomputed tomography, and the origin of the amniote crown group
The origin of amniotes was a key event in vertebrate evolution, enabling tetrapods to break their ties with water and invade terrestrial environments. Two pivotal clades of early tetrapods, the diadectomorphs and the seymouriamorphs, have played an unsurpassed role in debates about the ancestry of amniotes for over a century, but their skeletal morphology has provided conflicting evidence for their affinities. Using high-resolution X-ray microcomputed tomography, we reveal the three-dimensional architecture of the well preserved endosseous labyrinth of the inner ear in representative species belonging to both groups. Data from the inner ear are coded in a new cladistic matrix of stem and primitive crown amniotes. Both maximum parsimony and Bayesian inference analyses retrieve seymouriamorphs as derived non-crown amniotes and diadectomorphs as sister group to synapsids. If confirmed, this sister group relationship invites re-examination of character polarity near the roots of the crown amniote radiation. Major changes in the endosseous labyrinth and adjacent braincase regions are mapped across the transition from non-amniote to amniote tetrapods, and include: a ventral shift of the cochlear recess relative to the vestibule and the semicircular canals; cochlear recess (primitively housed exclusively within the opisthotic) accommodated within both the prootic and the opisthotic; development of a distinct fossa subarcuata. The inner ear of seymouriamorphs foreshadows conditions of more derived groups, whereas that of diadectomorphs shows a mosaic of plesiomorphic and apomorphic traits, some of which are unambiguously amniote-like, including a distinct and pyramid-like cochlear recess.
Rapid mechanical stimulation of inner-ear hair cells by photonic pressure
<p>Hair cells, the receptors of the inner ear, detect sounds by transducing mechanical vibrations into electrical signals. From the top surface of each hair cell protrudes a mechanical antenna, the hair bundle, which the cell uses to detect and amplify auditory stimuli, thus sharpening frequency selectivity and providing a broad dynamic range. Current methods for mechanically stimulating hair bundles are too slow to encompass the frequency range of mammalian hearing and are plagued by inconsistencies. To overcome these challenges, we have developed a method to move individual hair bundles with photonic force. This technique uses an optical fiber whose tip is tapered to a diameter of a few micrometers and endowed with a ball lens to minimize divergence of the light beam. Here we describe the fabrication, characterization, and application of this optical system and demonstrate the rapid application of photonic force to vestibular and cochlear hair cells.</p>
Figure 18 in Petrosal and inner ear anatomy and allometry amongst specimens referred to Litopterna (Placentalia)
Figure 18. Cerebellar views of virtually reconstructed petrosals (translucent) of UFRJ-DG 119-M, Proterotherium (MNHN- F-SCZ 205), Diadiaphorus (MNHN-F-SCZ 3), and Macrauchenia (MNHN-F-PAM 69) (from right to left), showing the relatively smaller size of the inner ear in larger specimens. Anterior to the left, ventral to the top.
Figure 19 in Petrosal and inner ear anatomy and allometry amongst specimens referred to Litopterna (Placentalia)
Figure 19. Allometric relationship between the inner ear height (IEH) and the petrosal (PET) size in a sample of 45 mammalian specimens (see Material and Methods and Table S2), with an equation of the regression line. Empty circles represent litoptern specimens.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.