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1,007 results for “three dimensional”
F I G U R E 1 in Three-dimensional migratory behaviour of European silver eels (Anguilla anguilla) approaching a hydropower plant
F I G U R E 1 Map of Sweden and the Ätran catchment, showing dams with or without fish passage solutions
F I G U R E 6 in Three-dimensional migratory behaviour of European silver eels (Anguilla anguilla) approaching a hydropower plant
F I G U R E 6 Correlation between relative swimming depths and inflow discharge for upstream- and downstream-swimming eels during the day and night in the river reach. Solid lines represent significant relationships, broken lines insignificant ones. Situation:, downstream day;, downstream night;, upstream day;, upstream night
Fig. 4 in First three-dimensional skull of the Middle Triassic mixosaurid ichthyosaur Phalarodon fraasi from Svalbard, Norway
Fig. 4. The phylogenetic tree of Ichthyosauria and the placement of PMO 235.393. Note that Parvipelvia has collapsed as this part of the tree is not the focus of the paper. Consensus tree of 19 MPTs with a length of 544. Consistancy Index = 0.373, Rentention Index = 0.778. Bremer support values displayed above nodes.
Fig. 1 in First three-dimensional skull of the Middle Triassic mixosaurid ichthyosaur Phalarodon fraasi from Svalbard, Norway
Fig. 1. Mixosaurid ichthyosaur Phalarodon fraasi (Merriam, 1910) PMO 235.393, from the Botneheia Formation, Middle Triassic of the Isfjorden area in Spitsbergen, Svalbard. A. Slab A in concretion, photograph (A1), line drawing (A2) showing the outline and identification of the visible bone elements. B. Hypothetical reconstruction of PMO 235.393.
Fig. 2 in First three-dimensional skull of the Middle Triassic mixosaurid ichthyosaur Phalarodon fraasi from Svalbard, Norway
Fig. 2. The segmented model of right lateral side of the skull of mixosaurid ichthyosaur Phalarodon fraasi (Merriam, 1910) PMO 235.393, from the Botneheia Formation, Middle Triassic of the Isfjorden area in Spitsbergen, Svalbard.
Fig. 3 in First three-dimensional skull of the Middle Triassic mixosaurid ichthyosaur Phalarodon fraasi from Svalbard, Norway
Fig. 3. The computed tomography rendered segmentation of rostral elements of mixosaurid ichthyosaur Phalarodon fraasi (Merriam, 1910) PMO 235.393, from the Botneheia Formation, Middle Triassic of the Isfjorden area in Spitsbergen, Svalbard. Right dentary and maxilla in lingual (A1) and labial (A2) views, right dentary (A3) in dorsal view, right maxilla in dorsal (A4) and lateral (A5) views. Note that the dorsal extent of the maxilla is not complete. Scale bars 10 mm.
Experimental data for: "Multi-slice electron ptychographic tomography for three-dimensional phase-contrast microscopy beyond the depth of field limits"
<p>This is the raw experimental data for the paper: "Multi-slice electron ptychographic tomography for three-dimensional phase-contrast microscopy beyond the depth of field limits"</p> <p>Now also including code to recreate figures, and data from alignment and multi-slice ptychography reconstructions.</p> <p>The data is in zarr format and can be read with the zarr python library. It also contains metadata in a dictionary. </p>
Data from: Twist and chew: three dimensional tongue kinematics during chewing in macaque primates
<p>Three-dimensional (3D) tongue movements are central to performance of feeding functions by mammals and other tetrapods, but 3D tongue kinematics during feeding are poorly understood. Tongue kinematics were recorded during grape chewing by macaque primates using biplanar videoradiography. Complex shape changes in the tongue during chewing are dominated by a combination of flexion in the tongue's sagittal planes and roll about its long axis. As hypothesized for humans, in macaques during tongue retraction the middle (molar region) of the tongue rolls to the chewing (working) side simultaneous with sagittal flexion, while the tongue tip flexes to the other (balancing) side. Twisting and flexion reach their maxima early in the fast close phase of chewing cycles, positioning the food bolus between the approaching teeth prior to the power stroke. Although 3D tongue kinematics undoubtedly vary with food type, the mechanical role of this movement—placing the food bolus on the post-canine teeth for breakdown—is likely to be a powerful constraint on tongue kinematics during this phase of the chewing cycle. The muscular drivers of these movements are likely to include a combination of intrinsic and extrinsic tongue muscles.</p>
Supplementary material: Picosecond pulse-shaping for strong three-dimensional field-free alignment of generic asymmetric-top molecules
<p><strong>Supplementary material to the manuscript <em>"Picosecond pulse-shaping for strong three-dimensional field-free alignment of generic asymmetric-top molecules"</em> by Terry Mullins, Evangelos T. Karamatskos, Joss Wiese, Jolijn Onvlee, Arnaud Rouzée, Andrey Yachmenev, Sebastian Trippel, and Jochen Küpper, <em>Nat Commun</em> 13, 1431 (2022). <a href="https://doi.org/10.1038/s41467-022-28951-z">https://doi.org/10.1038/s41467-022-28951-z</a>, arXiv: <a href="https://arxiv.org/abs/2009.08157">2009.08157 </a></strong></p> <ul> <li> <em><strong>simulations_part.z*</strong> </em>is split zip archive containing simulations data for indole molecule, such as files with rotational probability density distributions computed at different times <span class="math-tex">\(t=0..1500\)</span> ps during the laser pulse and field-free evolution, and example python scripts for data retrieval.</li> <li><strong><em>rawdata_part.z*</em></strong> is split zip archive containing raw experimental data.</li> <li><strong><em>analysis_scripts.zip</em></strong> is zip archive containing experimental analysis codes.</li> </ul> <p><strong>The <em>simulations_part.zip</em> contains the following files and folders:</strong></p> <ul> <li><em><strong>prob_density_euler_angles</strong></em> contains files <em>rotdens_av_<time>.gz</em> with simulated state-averaged rotational probability density distributions in terms of Euler angles for different times <time>, ranging from the beginning of the alignment laser pulse at <span class="math-tex">\(t=0\)</span> up to <span class="math-tex">\(t=1500\)</span> ps with a time step of 1 ps.<br> Calculations of probability density distributions were done using <a href="https://github.com/CFEL-CMI/richmol">Richmol</a> program.<br> The gzipped ASCII data files <em>rotdens_av_<time>.gz</em> contain in columns the values of the Euler angles <span class="math-tex">\(\phi,\theta,\chi\)</span> followed by the normalized probability density value.</li> <li><em><strong>prob_density_atoms_xyz</strong></em> contains files <em>monte_carlo_av_<time>.h5</em> with state-averaged rotational probability density distributions of all atoms in the indole molecule in terms of their Cartesian coordinates, for different times <time>, ranging from the beginning of the alignment pulse at <span class="math-tex">\(t=0\)</span> up to <span class="math-tex">\(t=1500\)</span> ps with a time step of 1 ps.<br> Structure of <em>monte_carlo_av_<time>.h5</em> HDF5 files:<br> Key Description<br> ----- ----------------<br> 'C10' - Cartesian coordinates of carbon atom no. 10<br> 'C11' - Cartesian coordinates of carbon atom no. 11<br> 'C12' - ...<br> 'C14' - ...<br> 'C3' - ...<br> 'C6' - ...<br> 'C7' - ...<br> 'C9' - ...<br> 'N4' - ...<br> 'H1-C3' - Cartesian coordinates of a vector pointing from carbon atom no. 3 to hydrogen atom no. 1<br> 'H13-C11' - ...<br> 'H15-C12' - ...<br> 'H16-C14' - ...<br> 'H2-N4' - ...<br> 'H5-C7' - ...<br> 'H8-C9' - ...<br> 'ref_vectors' - reference molecular-frame Cartesian coordinates of all atoms<br> 'x' - coordinates of the x-axis of Principal Axes of Inertia Frame<br> 'y' - coordinates of the y-axis of Principal Axes of Inertia Frame<br> 'z' - coordinates of the z-axis of Principal Axes of Inertia Frame<br> 'pol_x' - coordinates of the x-axis of Principal Axes of Polarizability Frame<br> 'pol_y' - coordinates of the y-axis of Principal Axes of Polarizability Frame<br> 'pol_z' - coordinates of the z-axis of Principal Axes of Polarizability Frame</li> <li><em><strong>indole_deflected_states.txt</strong></em> ASCII file contains initial populations of rotational states of indole in the deflected beam.<br> The following data is arranged in columns: <em>m, J</em>, <em>id</em>, <em>energy</em>, <em>normalized population</em>. The <em>J</em> and <em>m</em> are rotational quantum numbers of the total angular momentum and its <em>Z</em>-projection, the <em>id</em> number refers to the state's index in file <em>indole_energies_j0_j20.txt</em> listing rotational states of indole.</li> <li><em><strong>indole_data.py</strong></em> Python module provides basic functions to extract information from HDF5 data files <em>monte_carlo_av_<time>.h5</em>. It can also be used to compute alignment and orientation.</li> <li><em><strong>example_cos.py</strong></em> and <em><strong>example_dens.py</strong></em> Python scripts that demonstrate how to use <em>indole_data.py</em> module for computing and plotting alignment traces and a 2D projection of the probability density distribution, respectively.</li> <li><em><strong>monte_carlo.py</strong></em> Python script that was used to compute through Monte-Carlo sampling probability density distributions for Cartesian positions of atoms in indole (<em>monte_carlo_av_<time>.h5</em> files) using probability density distribution functions in Euler angles (outputs of Richmol program <em>rotdens_av_<time>.gz</em>).</li> </ul> <p><strong>The <em>analysis_scripts.zip</em> contains the following files and folders:</strong></p> <ul> <li><strong><em>H_Plus</em></strong> folder contains codes relevant for the analysis of H<sup>+</sup> ion data. <ul> <li><strong><em>analyse_full_alignment_scans.m</em></strong>: subtracts background and combines delay scan data sets together, takes account of errors.</li> <li><em><strong>calculate_resamped_df.m</strong></em>: called by <em>analyse_full_alignment_scans.m</em> to calculate the frequency sampling.</li> <li><em><strong>unique_mean.m</strong></em>: called by <em>analyse_full_alignment_scans.m</em> when combining data sets. Combines non-unique data points into a single data point.</li> </ul> </li> <li><em><strong>C_Plus2</strong></em> folder contains codes for the analysis of C<sup>2+</sup> ion data. The file descriptions are identical to those in the <em>H_Plus</em> directory.</li> <li><em><strong>intensity/calculate_intensity.m</strong></em>: calculates peak intensity of the laser pulse from measured parameters as well as statistical error.</li> <li><em><strong>intensity/compare_exp_sim.m</strong></em>: fits experimental and theoretical tomography and delay-dependent 2D projection values.</li> <li><em><strong>intensity/nir2hdf5_kHz.py</strong></em>: converts raw data files (from <em>rawdata_part.z*</em> archive<em>)</em> into hdf5 files.</li> </ul>
Raw Data for the article: Changes in the Transcriptome Profiles of Human Amnion-Derived Mesenchymal Stromal/Stem Cells Induced by Three-Dimensional Culture: A Potential Priming Strategy to Improve Their Properties
<p>Mesenchymal stromal/stem cells (MSCs) are believed to function in vivo as a homeostatic tool that shows therapeutic properties for tissue repair/regeneration. Conventionally, these cells are expanded in two-dimensional (2D) cultures, and, in that case, MSCs undergo genotypic/phenotypic changes resulting in a loss of their therapeutic capabilities. Moreover, several clinical trials using MSCs have shown controversial results with moderate/insufficient therapeutic responses. Different priming methods were tested to improve MSC effects, and three-dimensional (3D) culturing techniques were also examined. MSC spheroids display increased therapeutic properties, and, in this context, it is crucial to understand molecular changes underlying spheroid generation. To address these limitations, we performed RNA-seq on human amnion-derived MSCs (hAMSCs) cultured in both 2D and 3D conditions and examined the transcriptome changes associated with hAMSC spheroid formation. We found a large number of 3D culture-sensitive genes and identified selected genes related to 3D hAMSC therapeutic effects. In particular, we observed that these genes can regulate proliferation/differentiation, as well as immunomodulatory and angiogenic processes. We validated RNA-seq results by qRT-PCR and methylome analysis and investigation of secreted factors. Overall, our results showed that hAMSC spheroid culture represents a promising approach to cell-based therapy that could significantly impact hAMSC application in the field of regenerative medicine.</p>
Topological states in superlattices of HgTe class of materials for engineering three-dimensional flat bands
<p>In search of materials with three-dimensional flat band dispersions, using ab-initio computations we investigate how topological phases evolve as a function of hydrostatic pressure and uniaxial strain in two types of superlattices: HgTe/CdTe and HgTe/HgSe. In short-period HgTe/CdTe superlattices, our analysis unveils the presence of isoenergetic nodal lines, which could host strain-induced three-dimensional flat bands at the Fermi level without requiring doping, when fabricated, for instance, as core-shell nanowires. In contrast, HgTe/HgSe short-period superlattices are found to harbor a rich phase diagram with a plethora of topological phases. Notably, the unstrained superlattice realizes an ideal Weyl semimetal with Weyl points situated at the Fermi level. A small-gap topological insulator with multiple band inversions can be obtained by tuning the volume: under compressive uniaxial strain, the material transitions sequentially into a Dirac semimetal to a nodal-line semimetal, and finally into a topological insulator with a single band inversion.</p> <p>The provided repository contains data to reproduce the figures of the corresponding article.</p>
Three-dimensional in-situ imaging of single-grain growth in polycrystalline In2O3:Zr films
<p>Original data</p> <p>Here, we image a single-grain growth during the amorphous-to-polycrystalline transition in technologically relevant transparent conductive oxide (TCO) film of In<sub>2</sub>O<sub>3</sub>:Zr with <em>in-situ</em> Bragg coherent X-ray diffraction imaging.</p> <p>Data was obtained at 34ID-C end-station at Advanced Photon Source, Argonne National Laboratory (USA).</p> <p>Repository contains all raw datasets of the BCDI measurements, .spec files with corresponding meta-data, and .xlsx table with information on scan numbers related to annealing steps of the sample.</p>
Three-dimensional movement of the beak during seed processing in domestic canaries
<p>Many songbird species rely on seeds as a primary food source and the process of picking up, positioning, cracking, dehusking, and swallowing seeds is one of the most sophisticated tasks of the beak. Still, we lack understanding about how granivorous songbirds move their beak during the different phases of seed processing. In this study, we used multi-view high speed imaging to analyze the three-dimensional movement of the beak in feeding domestic canaries. Our analysis focuses on correlation of upper and lower beak, frequency of mandibulation, and direction of mandible movement in 3D space. We show that the correlation of maxilla and mandible movement differs among the phases of seed processing. Furthermore, we found that the beak moves at extremely high frequencies, up to 25 Hz, which resembles previously reported maximal syllable rates in singing canaries. Finally, we report that canaries use specific 3D mandible movements during the different phases of seed processing. Kinematic parameters do not differ between male and female canaries. Our findings provide an important biomechanical basis for better understanding the beak as a functional tool.</p>
Three-dimensional Digital Outcrop Models of the Tullig Sandstone, Western Irish Namurian Basin, Co. Clare, Ireland
<p>Tullig Sandstone is part of the Tullig Cyclothem, Western Irish Namurian Basin, Co. Clare, Ireland. The Tullig Sandstone is a prominent sandstone interval that represents an ancient fluvial-deltaic system. </p> <p>Outcrops of the Tullig Sandstone were surveyed by an unmanned aerial vehicle (UAV, DJI Mavic Pro Platinum™). Three-dimensional digital outcrop models were generated from images collected from UAV using Agisoft Metashape™.</p>
Data of: Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts
<p>These files are results obtained in<br><span><span><span><span>Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts</span></span></span></span><br>by Yoshito Hirata, Arisa H. Oda, Chie Motono, Masanori Shiro & Kunihiro Ohta.</p> <p>There are 33 files for the corresponding each reconstruction of three-dimensional chromosomone structures<br>for each cell.<br>There are 3D structures for 15 GM cells and 18 PBMC cells, which are obtained from the single cell Hi-C data of Tan et al. Science (2018).</p> <p>For each file, there are 6 columns:<br>The first column corresponds to the allele (0: maternal, 1: paternal)<br>The second column corresponds to the chromosome (1-22: chromosome's number, 23: X, 24: Y)<br>The third column corrsponds to the base point.<br>The fourth column, the fifth column and the sixth column correspond to x-, y-, and z-axes of our reconstruction.</p>
Three-dimensional surface scans of tooth surfaces of Sika deer from Torihama shell midden site
<p>Three-dimensional surface scans of tooth surfaces of Sika deer remains from Torihama shell midden site are saved in .sur format and surface analyses files in .mnt format, which are analyzed in:</p> <p>Sato, K., and Sato, T., and Kubo, M. O. "Reconstructing diets of hunted sika deer from Torihama shell midden site (ca. 6000 years ago) by dental microwear texture analysis" submitted to Frontiers in Ecology and Evolution. doi: 10.3389/fevo.2022.957038</p> <p>More details can be found in the information published in this paper.</p>
Three-Dimensional Thermoporoelastic Modeling of Hydrofracturing and Fluid Circulation in Hot Dry Rock: EGS Collab Experiment 1
<p>The data regarding the determined natural fractures, locations of monitoring devices, microseismic events, and well trajectories in EGS Collab Experiment 1.</p>
Raw data accompanying the manuscript "Cost-effective high-speed, three-dimensional live-cell imaging of HIV-1 transfer at the T cell virological synapse"
<p>These are the raw datasets used to generate the figures for the manuscript entitled "Cost-effective high-speed, three-dimensional live-cell imaging of HIV-1 transfer at the T cell virological synapse". The data files are 3D image stacks of a custom-built wide field deconvolution fluorescence microscope (.tif) and super-resolution structured illumination microscopy data (.dv) of Jurkat T cells transferring HIV-1 virus particles to previously uninfected primary T cells.</p>
Eddy Duck Data: Measured Three-Dimensional Structure of Surfzone Velocities
<p>This archive contains data from the 2011 EddyDuck experiment. Three-dimensional structure of surfzone velocity fields was measured using 12 horizontally-spaced Nortek Aquadopp current meters, each instrument measuring vertical profiles of water velocity. The experiment was conducted by folks from Washington State University and Oregon State University, with help from staff of the USACE's Duck Field Research Facility.</p> <p>Funding from the US National Sciences Foundation, Award OCE-1061692</p> <p>An in-review JGR-Oceans manuscript “Depth-Dependence of Nearshore Currents and Eddies” discusses the observations.</p> <p> </p> <p>Data are contained in two zip files.</p> <p>File summary.zip unzips to give a folder containing summary data in matlab 2015b format, and a pdf readme file explaining details.</p> <p>Folder full.zip unzips to give a folder containing full time-resolution data in ASCII format, and a readme file explaining details.</p> <p> </p> <p> </p> <p>Questions to steve_henderson@wsu.edu</p>
Data from: How many specimens make a sufficient training set for automated three dimensional feature extraction?
<p>Deep learning has emerged as a robust tool for automating feature extraction from 3D images, offering an efficient alternative to labour-intensive and potentially biased manual image segmentation methods. However, there has been limited exploration into the optimal training set sizes, including assessing whether artificial expansion by data augmentation can achieve consistent results in less time and how consistent these benefits are across different types of traits. In this study, we manually segmented 50 planktonic foraminifera specimens from the genus Menardella to determine the minimum number of training images required to produce accurate volumetric and shape data from internal and external structures. The results reveal unsurprisingly that deep learning models improve with a larger number of training images with eight specimens being required to achieve 95% accuracy. Furthermore, data augmentation can enhance network accuracy by up to 8.0%. Notably, predicting both volumetric and shape measurements for the internal structure poses a greater challenge compared to the external structure, due to low contrast differences between different materials and increased geometric complexity. These results provide novel insight into optimal training set sizes for precise image segmentation of diverse traits and highlight the potential of data augmentation for enhancing multivariate feature extraction from 3D images. </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.