Find research datasets worth reusing

opencc-by-sa-4.0Apr 2020View details →

The Hearpiece database of individual transfer functions of an openly available in-the-ear earpiece for hearing device research

We present a database of acoustic transfer functions of the Hearpiece, an openly available multi-microphone multi-driver in-the-ear earpiece for hearing device research. The database includes HRTFs for 87 incidence directions as well as responses of the drivers, all measured at the four microphones of the Hearpiece as well as the eardrum in the occluded and open ear. The transfer functions were measured in both ears of 25 human subjects and a KEMAR with anthropometric ears for five reinsertions of the device. We describe the measurements of the database and analyse derived acoustic parameters of the device. All regarded transfer functions are subject to differences between subjects as well as variations due to reinsertion into the same ear. Also, the results show that KEMAR measurements represent a median human ear well for all assessed transfer functions. The database is a rich basis for development, evaluation and robustness analysis of multiple hearing device algorithms and applications.

opencc-by-4.0Mar 2022View details →

Zellige example dataset: inner ear organoid epithelium

Inner ear organoid at day 14 of culture. 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: \(T_{A}=5, T_{otsu}=12, S_{min}=5, \sigma_{xy}=2, \sigma_{z}=1, T_{OSE1}=0.9, R_{1}=5, C_{1}=0.8, T_{OSE2}=0.1, R_{2}=10, C_{2}=0.8.\) 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. See the accompanying paper: Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool. Trébeau et al. 2022: <a href="https://doi.org/10.1101/2022.04.05.485876">https://doi.org/10.1101/2022.04.05.485876</a>

opencc-by-4.0Apr 2018View details →

A multiple model high-resolution head-related impulse response database for aided and unaided ears (HDF5 format)

The Multiple-Model High Resolution HRTF database is a collection of HRTFs measured using four different Head-and-Torso Simulators at high spatial resolution (2 degree azimuth and elevation).  The data here is stored in HDF5 files, the SOFA files are published in a separate dataset <a href="https://zenodo.org/record/2582553">doi:10.5281/zenodo.2582553</a>.

opencc-by-sa-4.0Mar 2019View details →

The PIRATE: an anthropometric earPlug with exchangeable microphones for Individual Reliable Acquisition of Transfer functions at the Ear canal entrance

We present the open design of the PIRATE, an anthropometric earPlug with exchangable microphones for Individual Reliable Acquisition of Transfer functions at the Ear canal entrance. Its outer shape is available in 5 sizes and provides a deep, tight and reproducible fit in virtually all human ears. The design includes a recess to accommodate a MEMS microphone. Thus, the same microphone can be conveniently used in different earplugs without losing accuracy, and the microphone can be removed for calibration. The PIRATE or previous versions of it have been utilized in several studies with more than 200 subjects From the provided model, the earplugs can be 3D printed, and only minor working steps are necessary before use. These steps are described in the documentation.   Reference: Denk F., Brinkmann F., Stirnemann S., Kollmeier B. (2019) "The PIRATE: an anthropometric earPlug with exchangeable microphones for Individual Reliable Acquisition of Transfer functions at the Ear canal entrance," Fortschritte der Akustik - DAGA, Rostock, Germany

opencc-by-4.0Oct 2024View details →

Influence of the cochlear partition's flexibility on the macro mechanisms in the inner ear

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>. It includes a finite element model of the inner ear, simulation results, and a Python script with code used for the analysis. <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>

opencc-by-4.0Sep 2021View details →

The IHA database of human geometries including torso, head and complete outer ears for acoustic research

This is the first version of the IHA database, which is being created in the project HAPPAA C1 funded by the Deutsche Forschungsgemeinschaft (DFG) – Projektnummer 352015383 - SFB 1330 C1. (https://uol.de/en/sfb-1330-hearing-acoustics) The database includes a subsample of 10 human geometries comprising the torso, head and the entire outer ear including the ear canal and eardrum. The data are available in two different 3D object formats: ply binary file, stl binary file.

opencc-by-4.0Sep 2021View details →

Avizo files of segmented middle ear of Eoarctos vorax

An exquisitely preserved skeleton (USNM 637259) of a basal ursoid is the basis of a monograph in Journal of Vertebrate Paleontology Memoir entitled "An Exquisitely Preserved Skeleton of Eoarctos vorax new gen. and sp. from Fitterer Ranch, South Dakota (early Oligocene) and Systematics and Phylogeny of North American Basal Arctoids (Carnivora, Caniformia)". This upload contains the Avizo files pertaining to a middle ear segmentation.

opencc-by-4.0Aug 2023View details →

Human Inner Ear Anatomy: Labeled Volume CT Data of Inner Ear Fluid Space and Anatomical Landmarks

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 \(99 \times 99 \times 99 \, \, \mathrm{\mu m}^3\). 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.   Usage Notes 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. The flat-panel volume CT raw data, labels and landmarks are saved in the HDF5-internal file structure using the respective group and datasets: <pre><code>raw/raw-0 label/label-0 landmark/landmark-0 landmark/landmark-1 landmark/landmark-2</code></pre> 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. 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: <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>   <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>   <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>

opencc-by-4.0Mar 2020View details →

EARS-NWC Metop-B dataset March 9, 2020, 08:00-08:19 UTC

EARS-NWC data, Metop-B, March 9th, 08:00 UTC to 08:19 UTC

opencc-by-4.0Mar 2019View details →

A multiple model high-resolution head-related impulse response database for aided and unaided ears (SOFA format)

The Multiple-Model High Resolution HRTF database is a collection of HRTFs measured using four different Head-and-Torso Simulators at high spatial resolution (2 degree azimuth and elevation).  The data here is stored in SOFA format, with the data identical to the HDF5 files in <a href="https://zenodo.org/record/1226873">doi:10.5281/zenodo.1226873</a>.

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Ecological niche models for American black bear, Rafinesque's big-eared bat, and timber rattlesnake

This data set contains rasters that are predictive environmental suitability maps for three wildlife species: the American black bear (Ursus americanus), Rafinesque's big-eared bat (Corynorhinus rafinesquii), and Timber rattlesnake (Crotalus horridus). Rasters for each species include: individual prediction maps for each of 5 ENMs (GBM: generalized boosting model, GLM: generalized linear model, MARS: multivariate adaptive regression spline, MX: maximum entropy, and RF: random forest), as well as the ensemble prediction map from all five ecological niche models (ENMs).

opencc-zeroAug 2020View details →

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Least-cost habitat linkages for American black bear, Rafinesque's big-eared bat, and timber rattlesnake.

This data set contains 3 shapefiles and associated files that map linkages, which are least-cost paths between adjacent habitat cores for three wildlife species in the Southeastern U.S. The species are: the American black bear (Ursus americanus), Rafinesque's big-eared bat (Corynorhinus rafinesquii), and Timber rattlesnake (Crotalus horridus). We mapped habitat cores based on c. 2006 land cover, then used LinkageMapper software to identify least-cost paths between them, and buffered the least-cost paths by 2.5 km using ArcGIS, for a total width of 5 km. The buffered least-cost paths are the linkages provided here. The attribute tables for these shapefiles contain fields that describe the importance of each linkage to the overall habitat connectivity network, contemporary and future average modeled habitat suitability within the linkage, change in average proportion suitable, percent of urban land within the linkage, percent of linkage that is protected for conservation, and categorical values for climate threat, whether the linkage was designated as highly important, protection status, and future urbanization threat.

opencc-zeroAug 2020View details →

opencc-by-4.0Jul 2015View details →

Figure 1 in Helminth fauna of the invasive American red-eared slider Trachemys scripta in eastern Spain: potential implications for the conservation of native terrapins

Figure 1. Sampling localities of the American red-eared slider, Trachemys scripta in eastern Spain. (A) Protected wetland 'Marjal de Peñíscola'; (B) 'Cabanes-Torreblanca' Natural Park; (C) Protected Landscape 'Desembocadura del Mijares'; (D) Protected wetland 'Marjal de Gandía'; (E) Site of Community Importance 'Marjal de La Safor'.

opencc-by-4.0Aug 2020View details →

Extensive qPCR analysis reveals altered gene expression in middle ear mucosa from cholesteatoma patients

Abstract The middle ear is a small and hard to reach compartment, limiting the amount of tissue that can be extracted and the possibilities for studying the molecular mechanisms behind diseases like cholesteatoma. In this paper 14 reference gene candidates were evaluated in the middle ear mucosa of cholesteatoma patients and two different control tissues. ACTB and GAPDH were shown to be the optimal genes for the normalisation of target gene expression when investigating middle ear mucosa in multiplex qPCR analysis. Validation of reference genes using c-MYC expression confirmed the suitability of ACTB and GAPDH as reference genes and showed an upregulation of c-MYC in middle ear mucosa during cholesteatoma. The occurrence of participants of the innate immunity, TLR2 and TLR4, were analysed in order to compare healthy middle ear mucosa to cholesteatoma. Analysis of TLR2 and TLR4 showed variable results depending on control tissue used, highlighting the importance of selecting relevant control tissue when investigating causes for disease. It is our belief that a consensus regarding reference genes and control tissue will contribute to the comparability and reproducibility of studies within the field.

Supplementary material for "The inner ear anatomy of glyptodonts and pampatheres (Xenarthra, Cingulata): functional and phylogenetic implications"

Left_inner_ear_Doedicurus.stl: digital model of the inner ear of Doedicurus in stl format. Left_inner_ear_Glyptodon.stl: digital model of the inner ear of Glyptodon in stl format. Left_inner_ear_Holmesina.stl: digital model of the inner ear of Holmesina in stl format. Left_inner_ear_Panochthus.stl: digital model of the inner ear of Panochthus in stl format. Left_inner_ear_Pseudoplohophorus.stl: digital model of the inner ear of Pseudoplohophorus in stl format. Matrix.nex: Matrix used to perform the phylogenetic analysis of xenarthrans based on inner ear characters. PC1, PC2, PC3 loadings plot.pdf: Figures showing the loadings of the morphometric variables in each of the first three principal components. Principal Components Analysis.xlsx: Spreadsheet  with the results of the Principal Components Analysis: PC summary, PC scores, and PC loadings. Table S1. Deviation from orthogonality.pdf: Deviation from orthogonality (log1090var), and agility categories from Spoor et al. (2007). Tree-PGLS.tre: 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.

opencc-by-4.0Apr 2024View details →

Presentation in ARO2024: Middle-ear sound transmission in cadaveric temporal bones

This is Bastian Baselt's presentation in ARO 2024. This data include presentations and related data. A subfolder "Data" includes categorized raw data and explanation for the data.

Fig. 3 in History And Modern Status Of The Black-Eared Wheatear, Oenanthe Hispanica (Passeriformes, Muscicapidae), In Ukraine

Fig. 3. Distribution of Oenanthe hispanica in Crimea in the 19th–21st centuries: 1 — 19th century, 2 — 20th century, 3 — 21st century; black FIgures are FIndings of the Oenanthe hispanica and Oenanthe pleschanka hybrids.

Fig. 5. A in History And Modern Status Of The Black-Eared Wheatear, Oenanthe Hispanica (Passeriformes, Muscicapidae), In Ukraine

Fig. 5. A hybrid of the Oenanthe hispanica and Oenanthe pleschanka from Crimea, Balaklava, June 13, 2019. Photo by A. Bazdyrev.

Fig. 2 in History And Modern Status Of The Black-Eared Wheatear, Oenanthe Hispanica (Passeriformes, Muscicapidae), In Ukraine

Fig. 2. Distribution of Oenanthe hispanica in Ukraine (according to data from 1984–2019): light circles are FIndings within the breeding area and black ones are FIndings of vagrant birds.

Fig. 4. A in History And Modern Status Of The Black-Eared Wheatear, Oenanthe Hispanica (Passeriformes, Muscicapidae), In Ukraine

Fig. 4. A hybrid of the Oenanthe hispanica and Oenanthe pleschanka from Crimea, Karadag, April 23, 1998; Exposition of the museum of the Karadag nature reserve. Photo by M. Beskaravainy.