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478 results for “3D data”
Example Data for 3D quantification of zebrafish cerebrovascular architecture
<p>Example data for:</p> <p>E. C. Kugler, J. Frost, V. Silva, K. Plant, K. Chhabria, T. J.A. Chico, P. A. Armitage</p> <p>3D quantification of zebrafish cerebrovascular architecture by automated image analysis of light sheet fluorescence microscopy datasets</p> <p>bioRxiv 2020.08.06.239905; doi: https://doi.org/10.1101/2020.08.06.239905</p> <p>Link: https://www.biorxiv.org/content/10.1101/2020.08.06.239905v2</p> <p><br> Code: https://github.com/ElisabethKugler/ZFVascularQuantification (doi:https://doi.org/10.5281/zenodo.3978278)</p> <p>Transgenic zebrafish 3dpf: Tg(kdrl:HRAS-mCherry)s916<br> Acquisition: Zeiss Z.1 light sheet microscope with a Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, sCMOS detection unit. <br> Activated pivot scan, dual-sided illumination and online fusion; <br> properties of acquired data are as follows: 0.7x zoom, 16bit image depth, 1920 x 1920px (approximately 0.33 x 0.33 µm) image size and minimum z-stack interval (approximately 0.5µm), <br> 561nm laser, LP560, and LP585.</p> <p>Data: <br> - tiff and MIPs<br> - TF: pre-processed with Sato enhancement<br> - TH: segmented with Otsu thresholding<br> - 512x512: downsampled<br> - Reg: intersample registration<br> - analysis: folder for quantification</p>
CT and 3D Data from: A large Middle Devonian eubrachythoracid 'placoderm' (Arthrodira) jaw from northern Gondwana
<p><em>Leptodontichthys ziregensis</em> is a newly described eubrachythoracid arthrodire from the Middle Devonian of Morocco. Only the posterior superognathal is preserved, it possesses features which were, so far, seen in Late Devonian forms. The jaw bone presents two sets of teeth, one lateral and one posterior, with dentinous tissue, pulp cavities and vascular canals preserved. The CT scans provided here are the ones used for the study. The complete jaw data was used for the overall study and the closeup data was used for the segmentation of the teeth. The ply data is provided to provide the information extracted by the authors during the study.</p>
Data from: The effects of aging on neuropil structure in mouse somatosensory cortex—A 3D electron microscopy analysis of layer 1
This study has used dense reconstructions from serial EM images to compare the neuropil ultrastructure and connectivity of aged and adult mice. The analysis used models of axons, dendrites, and their synaptic connections, reconstructed from volumes of neuropil imaged in layer 1 of the somatosensory cortex. This shows the changes to neuropil structure that accompany a general loss of synapses in a well-defined brain region. The loss of excitatory synapses was balanced by an increase in their size such that the total amount of synaptic surface, per unit length of axon, and per unit volume of neuropil, stayed the same. There was also a greater reduction of inhibitory synapses than excitatory, particularly those found on dendritic spines, resulting in an increase in the excitatory/inhibitory balance. The close correlations, that exist in young and adult neurons, between spine volume, bouton volume, synaptic size, and docked vesicle numbers are all preserved during aging. These comparisons display features that indicate a reduced plasticity of cortical circuits, with fewer, more transient, connections, but nevertheless an enhancement of the remaining connectivity that compensates for a generalized synapse loss.
Data from: The dipnoan buccal pump reconstructed in 3D and implications for air breathing in Devonian lungfishes
Lungfishes are known for, and indeed take their name from, their bimodal respiratory abilities. All three extant genera can use their lungs to extract oxygen from the atmosphere, although their reliance upon this capability differs among taxa. Lungs are considered primitive for the Osteichthyes, however the distinctive buccal pump mode of air gulping exhibited by extant lungfishes appears to be a specialization. It is associated with a number of derived skeletal characters (cranial ribs, long parasphenoid stalk, midline gap between palatal tooth plates) that first appeared during the Devonian. These have been described individually, but in no Devonian lungfish has their three-dimensional (3D) spatial relationship been reconstructed and analyzed. Here we present the 3D morphology of Rhinodipterus, a Mid-Late Devonian lungfish from Australia and Europe, based on synchrotron tomography and conventional microtomography scans. Unlike less crownward contemporaneous lungfishes such as Griphognathus and Chirodipterus, Rhinodipterus has a full set of skeletal buccal pump components that can be directly compared to those of extant lungfishes, suggesting that it made more extensive use of air breathing than other Gogo or Bergisch Gladbach genera. This is interesting in relation to the environmental context as Gogo and Bergisch Gladbach are both marine, contrasting with the frequently hypoxic tropical to subtropical fresh water environments inhabited by modern lungfishes. The evolution of buccal pump-supported lung ventilation was evidently not necessarily associated with a transition to non-marine habitats.
Data from: The evolution of skull and body shape in Triturus newts reconstructed from 3D morphometric data and phylogeny
To explore the relationship between morphological change and species diversification, we reconstructed the evolutionary changes in skull size, skull shape, and body elongation in a monophyletic group of eight species that make up salamander genus Triturus. Their well-studied phylogenetic relationships and the marked difference in ecological preferences among five species groups makes this genus an excellent model system for the study of morphological evolution. The study involved three-dimensional imagery of the skull and the number of trunk vertebrae, in material that represents the morphological, spatial, and molecular diversity of the genus. Morphological change largely followed the pattern of descent. The reconstruction of ancestral skull shape indicated that morphological change was mostly confined to two episodes, corresponding to the ancestral lineage that all crested newts have in common and the Triturus dobrogicus lineage. When corrected for common descent, evolution of skull shape was correlated to change in skull size. Also, skull size and shape, as well as body shape, as inferred from the number of trunk vertebrae, were correlated, indicating a marked impact of species' ecological preferences on morphological evolution, accompanied by a series of niche shifts, with the most pronounced one in the T. dobrogicus lineage. The presence of phylogenetic signal and correlated evolutionary changes in skull and body shape suggested complex interplay of niche shifts, natural selection, and constraints by a common developmental system
Scripts and raw data for comparing 2D vs 3D image analysis of zebrafish embryo microscopic data
<p>Raw data and MatLab scripts used for image analysis of RNA polymerase II with serine 5 phosphorylation in the C-terminal domain (CTD) of the subunit 1 (Pol II Ser5P) in a fixed zebrafish embryo, comparing a 2D vs 3D approach to segment out the Pol II Ser5P clusters. Pol II Ser5P was labeled by immunofluorescence, microscopy images were acquired by instant-SIM microscopy and analyzed using MatLab scripts and the bioformats importer.</p>
Data for "MorphVAE: Generating Neural Morphologies from 3D-Walks using Variational Autoencoder with Spherical Latent Space"
<p>The reconstructions and the processed data that accompany the publication </p> <p><strong>MorphVAE: Generating Neural Morphologies from 3D-Walks using a Variational Autoencoder with Spherical Latent Space</strong></p> <p>Sophie Laturnus, Philipp Berens</p> <p>https://www.biorxiv.org/content/10.1101/2021.06.14.448271v1</p> <p>doi: https://doi.org/10.1101/2021.06.14.448271</p>
Data from: A new dimension in documenting new species: high-detail imaging for myriapod taxonomy and first 3D cybertype of a new millipede species (Diplopoda, Julida, Julidae)
We review the state-of-the-art approaches currently applied in myriapod taxonomy, and we describe, for the first time, a new species of millipede (Ommatoiulus avatar n. sp., family Julidae) using high-resolution X-ray microtomography (microCT) as a substantive adjunct to traditional morphological examination. We present 3D models of the holotype and paratype specimens and discuss the potential of this non-destructive technique in documenting new species of millipedes and other organisms. The microCT data have been uploaded to an open repository (Dryad) to serve as the first actual millipede cybertypes to be published.
Data from: Are 2D space-use analyses adapted to animals living in 3D environments? A case study on a fish shoal
Methodologies enabling the monitoring of animal movement and behavior in 3-dimensions (3D; x, y, z, the latter accounting for the vertical dimension) are becoming increasingly accessible and can be deployed on entire groups of animals inhabiting 3D habitats. When 2-dimensional (2D; x, y) space-use analyses are used on such groups, their spatial organization is represented as a planar projection of individuals' space-use. Movement on the vertical dimension is ignored and could biased ecological inference made from the spatial structure of the group. We used a digital imaging technique to track movements and feeding behavior of individual animals within a free-range aggregation of juvenile drift-feeding fish (Galaxias anomalus) in 3D and at fine spatiotemporal scales. We estimated spatiotemporal overlap of space-use and feeding territories between group-members using 2D (x, y) and 3D spatial analysis to: (1) describe the spatial structure of the group, (2) identify patterns of resource partitioning, and (3) investigate the relationship between space-use overlap and feeding behavior. We found that overlapping ratios of space-use and feeding territories were over-estimated in 2D, while 3D analysis of space-use provided evidence of spatial partitioning between group-members. We also found that, regardless of the computation used, the overlapping ratios of space-use were positively correlated with overlapping ratios of feeding territories while no effect was found on feeding activity. In conclusion, whilst 3D analysis provided valuable information on the spatial structure of a group, inferences on the ecological function of space-use can also be obtained from 2D analysis.
Data from: Integrating 2D and 3D shell morphology to disentangle the palaeobiology of ammonoids: a virtual approach
Based on data derived from computed tomography, we demonstrate that integrating 2D and 3D morphological data from ammonoid shells represents an important new approach for investigating the palaeobiology of ammonoids. Characterization of ammonite morphology has long been constrained to 2D data, with only a few studies collecting ontogenetic data in 180° steps. Here we combine this traditional approach with 3D data collected from high-resolution nano-computed tomography. Ontogenetic morphological data on the hollow shell of a juvenile ammonite Kosmoceras (Jurassic, Callovian) was collected. 2D data was collected in 10° steps and show significant changes in shell morphology. Preserved hollow spines show multiple mineralized membranes never reported before, representing temporal changes in the ammonoid mantle tissue. 3D data show that chamber volumes do not always increase exponentially, as was generally assumed, but may represent a proxy for life events, such as stress phases. Furthermore, chamber volume cannot be simply derived from septal spacing in forms comparable to Kosmoceras. Vogel numbers represent a 3D parameter for chamber shape, and those for Kosmoceras are similar to other ammonoids (Arnsbergites, Amauroceras) and modern cephalopods (Nautilus, Spirula). Two methods to virtually document the suture line ontogeny, used to document phylogenetic relationships of larger taxonomic entities, were applied for the first time and present a promising alternative to hand drawings. The curvature of the chamber surfaces increases during ontogeny due to increasing strength of ornamentation and septal complexity. As this may allow for faster handling of cameral liquid, it could compensate for decreasing SA/V ratios through ontogeny.
3D Cryo Soft X-ray Transmission Microscopy data of Intact Thick Cells for Membrane Segmentation and Quantification
<p>The datasets used for evaluation of the proposed method in R. Cárdenes and C. Zhang et al. "3D Membrane Segmentation and Quantification of Intact Thick Cells using Cryo Soft X-ray Transmission Microscopy: A Pilot Study", PloS One, 2017. (DOI: 10.1371/journal.pone.0174324)</p>
TRUST 3D Dust RT Slab Benchmark Data
<p>Output global SEDs and images at selected wavelengths for the Slab benchmark of the TRUST collaboration. TRUST is a suite of benchmarks for 3D dust radiative transfer codes in astronomy. </p> <p>Paper describing the TRUST Slab benchmark is Gordon et al. (2017, A&A, 603, 114; http://adsabs.harvard.edu/abs/2017A&A...603A.114G)</p> <p>More details on TRUST at http://ipag.osug.fr/RT13/RTTRUST/.</p> <p>Code to make plots using this data at: https://github.com/karllark/trust_slab</p>
Data of 3D MHD Simulation for manuscript "Characteristics of Transpolar Arc Motion and its Corresponding Magnetospheric Dynamic Process"
<p>Data of 3D MHD Simulation for manuscript "Characteristics of Transpolar Arc Motion and its Corresponding Magnetospheric Dynamic Process"</p> <p>There are 6 types of data files:</p> <p>1) -3)MHD simulation results for FAC, plasma density, and temperature, projected at the x = -40RE position, with the viewpoint from the magnetotail towards the earth</p> <p>4) FAC mapping.rar. These data are the parametters in the plane of about Z=0 RE, which were mapped to the 7.2 Re, along the magnetic field lines.</p> <p>5) The simulation results of the model are plotted for FAC on Z=0RE.</p> <p>The results of the above data simulation plot are from 20171115 23:00 UT to 20171116 02:00 UT.</p> <p>6) XXBDd0142.rar, which is full 3D Simulation data at 2017.11.16 01:22 UT;</p> <p>All of these data include the following parameters:</p> <p>time, x, y, z, logrho, Vx, Vy, Vz, Bx, By, Bz, Pr, Jx, Jy, Jz, Edj</p> <p>7) SSUSI data at 2017.11.16.</p> <p> </p>
An efficient 3D inversion scheme for continental scale Magnetotelluric data
<p>These zipped file contain 3D magnetotelluric dataset (synthetic and SAMTEX field data) and corresponding inverted model obtained using AP3DMT(RB) code<br>(Radiation Boundary version of the AP3DMT code) for the publications “3D inversion scheme for high-resolution analysis of continental scale Magnetotelluric<br>data”. </p>
Input Data for A Fast Surrogate Model for 3D-Earth Glacial Isostatic Adjustment using Tensorflow (v2.8.0) Artificial Neural Networks
<p>Training datasets for the manuscript A Fast Surrogate Model for 3D-Earth Glacial Isostatic Adjustment using Tensorflow (v2.8.0) Artificial Neural Networks. Two separate datasets are contained for training the ANNs: the 3D-spherically-symmetric (SS) rate-of-change of relative sea level (ROCRSL) and the 3D-SS rate of change of radial displacement (ROCRAD) as a function of SS profiles. Two other datasets contain RSL projections from the explicit (i.e. Seakon 3D - Seakon SS + NMSS ) model and the NMSS model, labelled Seakon_plus_NMSS_RSL and NMSS respectively.</p> <p>Filenames denote the structure of the SS profile: </p> <p>???_?.??_??.*.csv = LT_UMV_LMV.*.{csv,nc}<br> </p> <p>LT = elastic lithosphere thickness (km)</p> <p>UMV = upper mantle viscosity (1E21 Pa s)</p> <p>LMV = lower mantle viscosity (1E21 Pa s)</p> <p>i.e. 96_0.5_10.seakon_S40RTS_lr18-SS.rrad.roc.r360x180.P5.density_wSSRRADROC.csv.bz2 has the SS profile</p> <p>96km elastic lithosphere, 0.5E21 Pa s upper mantle viscosity, 10E21 Pa s lower mantle viscosity</p> <p> </p> <p>The columns of the input files are as follows:</p> <p>LT, UMV, LMV, longitude, latitude, time(t=0), ice(t=0), SS_ROC_RSL (t=0), time(t=-1), ice(t=-1), time(t=-2), ice(t=-2), time(t=-3), ice(t=-3), time(t=-4), ice(t=-4), 3D-SS_ROC_RSL(t=0)</p> <p>units for the above are as follows:</p> <p>km, 1E21 Pas, 1E2 Pas, degrees east (0->360), degrees (-180->180), days since 2000, m, mm/year, days since 2000, m, days since 2000, m, days since 2000, m, days since 2000, m, mm/year</p> <p>where 'days since 2000' assumes exactly 365.25 days per year.</p>
Updated Data corresponding to a study on 'Rapid Patient-Specific FEM Meshes from 3D iPhone Scans'
Open the record for dataset details and reuse information.
3D Point Clouds of Trees and Apple Fruit Annotated with Thermal Data
<p>The data set captures four measurements during fruit growth: 06/28/2022 (15:00), 07/12/2022 (15:00), 09/01/2022 (15:00), 09/06/2022 (13:00)</p> <p>Additionally, diurnal courses are provided for three days: </p> <table> <tbody> <tr> <td> <p>Date</p> </td> <td> <p>Time</p> </td> </tr> <tr> <td> <p>09/21</p> </td> <td> <p>07:00, 08:00, 10:00, 12:00, 13:00, 18:00</p> </td> </tr> <tr> <td> <p>09/22</p> </td> <td> <p>07:00, 08:00, 10:00, 12:00, 13:00, 18:00</p> </td> </tr> <tr> <td> <p>10/05</p> </td> <td> <p>06:30, 07:00, 09:00, 10:00, 11:00, 16:00</p> </td> </tr> </tbody> </table> <p> </p> <p>The data set was measured in Blocks (A-D) of trees (T) on apple (A) fruit and is stored as compressed zip files, capturing raw, preprocessed, and manually recorded reference (ground truth) data.</p> <p>1. zip files entitled Raw_YYYY_MM_DD_Block[A-C]-[R, L] for seasonal data and Raw_YYYY_MM_DD_BlockD-[R, L]_Hour__:__ for diel data</p> <p>- raw data of LiDAR 3D point clouds - txt files</p> <p>- raw image data by thermal camera - txt files</p> <p>2. zip files entitled YYYY_MM_DD or DailyAcquisitions:</p> <p>- preprocessed (merged) sensor data of temperature-annotated 3D point clouds of canopies - csv files</p> <p>- preprocessed data, capturing manually segmented point clouds of temperature-annotated fruit - txt files</p> <p>3. Microsoft Excel files entitled References and Weather data:</p> <p>- raw data, representing reference data of fruit - xlsx file</p> <p>- raw data of weather conditions - xlsx file</p>
Data and code for "Quasiparticle effects in magnetic-field-resilient 3D transmons"
<p>This folder contains all data files and Jupyter notebooks needed to recreate the figures of our publication, <br>"Quasiparticle effects in magnetic-field-resilient 3D transmons",<br>written by J. Krause, G. Marchegiani, L. M. Janssen, G. Catelani, Yoichi Ando, and C. Dickel</p> <p>Measurements were done with quantify-core (https://quantify-os.org/docs/quantify-core/)</p> <p>Required python packages are quantify-core (tested to run with version 0.7.4) and all its dependencies, as well as cmcrameri (colormaps used for plots).<br>Qutip is used for master equation solving and Hamiltonian modeling (used version 4.7.5) and hmmlearn (version 0.3.2) for fitting gaussian hidden-markov-models.<br>From a clean conda environment one should just install the above 4 packages and it should work.</p> <p>Content:<br>Data/ <br>Contains the plotted measurement data used in the figures of the paper mostly in csv format.<br>The datasets are loaded and plotted in the respective notebooks for all figures. </p> <p>Data/quantify_datasets/<br>Contains a few quantify datasets (raw data format of quantify measurements)</p> <p>Data/20220710_parity_paper_device_afm/<br>Contains .tiff images and .txt files with AFM data of the device</p> <p>Figures/<br>Contains all paper figures as .pdf files</p> <p>Fits/transmon_spectrum_including_EJ_harmonics<br>Contains some auxiliary fit results so the fits of flux arcs do not have to be repeated.</p> <p>Fits/Gap_vs_Bpar<br>Contains numerical results for the superconducting gap Delta as a function of magnetic field for aluminum films of different thickness.<br>Used to check the cavity data and not used for other modeling.<br>Imported in Jupyter_notebooks/models_transmon_spectrum_including_higher_harmonics.py</p> <p>Jupyter_notebooks/<br>Contains the jupyter notebooks with the code that creates the figures including the relevant calculations and fits and the loading of the data.<br>The notebook name gives the figure(s) it creates.<br>There are several auxiliary .py files and two notebooks that do not make paper figures:</p> <p>Jupyter_notebooks/fit_params.py<br>Contains the fit parameters for the quasiparticle modeling and the transmon spectrum</p> <p>Jupyter_notebooks/models_qp_dynamics.py<br>Contains the functions for quasiparticle modeling vs field and temperature.</p> <p>Jupyter_notebooks/models_transmon_spectrum_including_higher_harmonics.py<br>Contains the models for the field dependent spectrum</p> <p>Jupyter_notebooks/models_cavity_transmon_interaction.py<br>Contains qutip model for the fitting of the transmon-cavity Hamiltonian to estimate the bare-dressed changes.</p> <p>Jupyter_notebooks/fit_quasiparticle_model.ipynb<br>Notebook that shows how the quasiparticle model can be fit to the data<br>Takes a bit longer to execute</p> <p>Jupyter_notebooks/fit_cavity_transmon_interaction.ipynb<br>Looks at a resonator-transmon model to understand the bare-dressed difference and estimate the coupling.<br>Not really used in the paper, except to estimate G. </p>
MRI data of 3D radial multi-echo spin-echo acquisition of the human brain at 3T with and without deliberate motion
<p>Radial 3D multi-echo spin echo acquisition of a human brain acquired with a house made sequence on a Prisma Siemens 3T MRI scanner. </p> <p>The data have been converted in ISMRMRD format. </p> <p>Two raw datasets are available, one with deliberate motion and one without. </p> <p>The sequence allows for retrospective motion correction based on self-navigation. </p> <p>The images can be reconstructed with the code available on Github: https://github.com/nadegecorbin/Reco_MESE_RAD.git</p> <p>Reconstructed images and associated T2 maps are also provided in the folder "Reconstruction".</p> <p>For the motion case, intermediate images are stored in "Motion/Moco/RecoTRImages", the corrected echoes are in "Motion/Moco/RecoEchoes". Echo images without correction are in "Motion/Nomoco/RecoEchoes". </p> <p>For the No motion case, only data without motion correction are reconstructed and are located in "Nomotion/Nomoco/Recoechoes"</p> <p>A manuscript describing the method is under submission. </p> <p> </p>
Research data for: Direct DLP-based 3D-printing of metallopolymers featuring shape-memory abilities
<p><span>This study presents for the first time the direct digital light processing (DLP) based three-dimensional (3D) printing of metallopolymers featuring different kinds of metal complexes. 2-Phenoxyethyl acrylate and ligand-containing monomers based on terpyridine, and triphenylmethyl(trt)‑histidine are utilized. After successful complexation of zinc(II) and nickel(II) salts, respectively, within the monomer mixture the polymerization <em>via</em> photo-induced printing is performed. The hereby obtained smart materials can be printed in any form ranging from simple rectangular rods to complex hollow structures. Inductively coupled plasma optical emission spectroscopy (ICP-OES) and Fourier-transform (FT) Raman spectroscopy reveal the successful imbedding and implementation into the polymeric structure. Additionally, an imaging across the 3D-printed structure could be performed indicating the equal distribution of the complexes in the structure. Furthermore, the 3D-printed specimens feature excellent shape-memory behavior. Thermo-mechanical analysis (TMA) reveals fixity rates after mechanical deformation up to 100% and recovery rates up to 99%.</span></p> <p><span> </span></p>
ScienceDex guides
Understand access before you commit
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.