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438
datasets available to search
ShareScore release 0.9.0
Dataset results
438 results for “3D imaging”
3D co-registration of ultra-low-field and high-field magnetic resonance images (data)
<p>Dataset used for "3D co-registration of ultra-low-field and high-field magnetic resonance images" submitted to PlosOne.</p>
Data for Matlab package locFISH to simulate realistic 3d smFISH images
<p>Different data-sets needed by the Matlab package locFISH. locFISH allows the simulation and analysis of realistic single molecule FISH (smFISH) images.</p> <p><strong>data_simulation.zip</strong><br> Contains all necessary data to simulated smFISH images. Specifically, the zip archive contains a library of 3D cell shapes, realistic imaging background, and a simulated PSF (Point Spread Function). </p> <p><strong>GAPDH.zip</strong><br> Contains the smFISH data of GAPDH and the corresponding analysis results, which were used to create the library of cell shapes provided in data_simulation.zip </p> <p>For more details on these data and how do to use them, please consult the detailed user-manual provided with <strong>locFISH</strong>, available at</p> <p>https://bitbucket.org/muellerflorian/fish_quant</p>
Semi-Supervised Pre-trained Foundation Model for 3D Structural Feature Analysis of Seismic Images
<p>Codes, trained model, and datasets for the paper "Semi-Supervised Pre-trained Foundation Model for 3D Structural Feature Analysis of Seismic Images".</p>
3D super-resolution datasets associated with the paper "Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet"
<p>3D single-molecule super-resolution datasets corresponding to reconstructions shown in <em>Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet</em> by Saliba & Gagliano, Gustavsson et. al.</p>
X-ray tomography 3D image dataset of natural fibre reinforced polypropylene
<p>Natural fibre composites have potential sustainability benefits over traditional composites, but their irregular shapes and mechanical properties require more thorough examination compared to glass or carbon fibre composites. 3D X-ray imaging allows for non-destructive examination of the structure and shape. The dataset includes 3D images obtained using micro X-ray computed tomography of natural fibre composites. The images provide valuable insights into the material's characteristics. Since there is limited open-access 3D image data on natural fibre composites, this dataset lays the groundwork for future image analysis and numerical modelling.</p>
Outputs from new methods for 3D+time cell image segmentation and tracking
<p>Segmentation and tracking of 3D+time microscopy images of cell nuclei within the zebrafish pectoral fin.</p> <p>The file named 7_cells_moving_in_70_frames_orig.avi is a 70-frame video of a group of cells moving in time, the file named 7_cells_moving_in_70_frames.avi has the result of 4D segmentation, using our new segmentation methods, for seven cells (colored black) moving in time, and the file _tracking_of_7_cell_in_70_frames.mp4 has the tracking of these seven cells. </p> <p>Additionally, the file named group_of_cells_moving_in_70_frames_orig.avi is a 70-frame video of a group of cells moving in time, the file named group_of_cells_moving_in_70_frames.avi has the result of 4D segmentation, using our new segmentation methods, for the group of cells (colored black) moving in time and the file _tracking_of_group_of_cell_in_70_frames.gif has the tracking of this group of cells. </p>
Dataset - Impact of 3D radiative transfer on airborne NO2 imaging remote sensing over cities with buildings
<p>This dataset was created by Marc Schwaerzel (marc.schwaerzel@empa.ch) and is intended to get along with the Schwaerzel et al. (2021) AMT publication (amt-2020-146) . The data and the data structure is described in the<em> <strong>readme.md </strong></em>text file.</p> <p>The dataset contains:</p> <p>- libRadtran output (radiances and AMFs)</p> <p>- Synthetic SCDs</p>
UAV RGB imagery dataset captured at nadir and oblique angles over pistachio trees in Spain, including images, GCPs, 3D point cloud and orthomosaic.
<p>The dataset comprises 248 images taken in two flights on 29 July 2021 over a pistachio orchard in Spain. In addition, GCPs (ground control points) were collected to improve the photogrammetric process accuracy. The photos were taken using a UAV DJI Phantom Advance quadcopter equipped with a DJI FC6310 RGB 20-megapixel camera. The first flight mission was planned to take nadir images (-90º gimbal pitch degree), whereas the second flight was scheduled to take oblique images (-60º gimbal pitch degree), both at 55 metres above the ground. In addition, the images were used to generate a 3D point cloud, DEM and orthomosaic, which were included in the dataset.This dataset is useful for precision agriculture researchers interested in photogrammetric reconstruction.</p>
Supplementary videos for the "Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture" manuscript
<p>Supplementary videos for preprint manuscript: </p> <p><em>Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture</em><br> Liuba Dvinskikh, Hugh Sparks, Liliana Brito, Kenneth T MacLeod, Sian E Harding, Christopher Dunsby<br> bioRxiv 2023.01.28.526043; doi: https://doi.org/10.1101/2023.01.28.526043</p> <p>All videos have been rendered with JPEG compression.</p> <p>Shortened video captions (Please see supplementary information document for full caption)<br> <strong>Video 1:</strong> 3D LSFM timelapse of hiPSC-CM undergoing spontaneous calcium transients. <br> <strong>Video 2:</strong> Widefield transillumination timelapse of hiPSC-CM and adult-CM <br> <strong>Video 3:</strong> Widefield fluorescence timelapse of hiPSC-CM and adult CM with synchronized spontaneous calcium transients. <br> <strong>Video 4a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients. <br> <strong>Video 4b</strong>: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients. <br> <strong>Video 5a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients in a sample without NBleb. <br> <strong>Video 5b</strong>: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture without NBleb undergoing synchronized spontaneous transients. <br> <strong>Video 6a</strong>: 3D LSFM timelapse of hiPSC-CM and adult-CM co-culture undergoing synchronized spontaneous transients in a sample treated with NBleb. <br> <strong>Video 6b:</strong> Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture with NBleb undergoing synchronized spontaneous transients. <br> <strong>Video 7a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 0 co-culture undergoing synchronized spontaneous transients in a sample without NBleb. <br> <strong>Video 7b: </strong>Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 0 co-culture without NBleb. </p> <p> </p>
Synthesis of large scale 3D microscopic images of 3D cell cultures for training and benchmarking
<p>Accompaning data to the paper:</p> <p>Synthesis of large scale 3D microscopic images of 3D cell cultures for training and benchmarking</p>
3D images of ovule primordia development in Zea mays - Part II
<p>This image resource describes the development of ovule primordia of <em>Zea mays</em>, in 3D and at cellular resolution. The images were segmented using ImarisCell (Bitplane, Switzerland) and annotated as described in the associated manuscript Ouedraogo et al. (2023) Frontiers in Plant Science. DOI: 10.3389/fpls.2023.1174171</p> <p><em>Zea mays</em> (B73 genotype) floret meristem and ovule primordia were stained using a cell wall and nuclear dyes, cleared using Clearsee solution (Kurihara et al., 2015), imaged using multiphoton microscopy and processed for segmentation in ImarisCell (Bitplane) as decribed in Mendocilla Sato et al., 2017. The .ims files also contains Surfaces objects for 3D rendering of specific cells or organs, used for quantitative analysis as described in the associated manuscript.</p> <p>Each file corresponds to an individual ovule primordia or floret meristem, with file names corresponding to ovule ID as described in Supplementary Dataset 1 of the associated manuscript Ouedraogo et al. (2023) Frontiers in Plant Science. DOI: 10.3389/fpls.2023.1174171</p>
3D images of ovule primordia development in Zea mays - Part I
<p>This image resource describes the development of ovule primordia of <em>Zea mays</em>, in 3D and at cellular resolution. The images were segmented using ImarisCell (Bitplane, Switzerland) and annotated as described in the associated manuscript Ouedraogo et al. (2023) Frontiers in Plant Science. DOI: 10.3389/fpls.2023.1174171</p> <p><em>Zea mays</em> (B73 genotype) floret meristem and ovule primordia were stained using a cell wall and nuclear dyes, cleared using Clearsee solution (Kurihara et al., 2015), imaged using multiphoton microscopy and processed for segmentation in ImarisCell (Bitplane) as decribed in Mendocilla Sato et al., 2017.</p> <p>Each file corresponds to an individual ovule primordia or floret meristem, with file names corresponding to ovule ID as described in Supplementary Dataset 1 of the associated manuscript Ouedraogo et al. (2023) Frontiers in Plant Science. DOI: 10.3389/fpls.2023.1174171</p> <p> </p>
3D images of ovule primordia development in Zea mays - Part III
<p>This image resource describes the development of ovule primordia of <em>Zea mays</em>, in 3D and at cellular resolution. The images were segmented using ImarisCell (Bitplane, Switzerland) and annotated as described in the associated manuscript Ouedraogo et al. (2023) Frontiers in Plant Science. DOI: 10.3389/fpls.2023.1174171</p> <p><em>Zea mays</em> (B73 genotype) floret meristems and ovule primordia were stained using cell wall and nuclear dyes, cleared using Clearsee solution (Kurihara et al., 2015), imaged using multiphoton microscopy and processed for segmentation in ImarisCell (Bitplane) as decribed in Mendocilla Sato et al., 2017. The .ims files also contains Surfaces objects for 3D rendering of specific cells or organs, used for quantitative analysis as described in the associated manuscript.</p> <p>Each file corresponds to an individual ovule primordia or floret meristem, with file names corresponding to ovule ID as described in Supplementary Dataset 1 of the associated manuscript Ouedraogo et al. (2023). Frontiers in Plant Science. DOI: 10.3389/fpls.2023.1174171</p>
Imaging data from "Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD"
<p>3D 20ms, 3D 500ms and 2D dCas9 raw videos, localisation, tracking and trajectory analysis data</p> <p>From 'Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD" (2021). Biorxiv. https://doi.org/10.1101/2020.04.03.003178</p>
Images and 3D digitisations of Branding Heritage
<p>These files are 3D digitisations and images of Branding Heritage</p>
2D and 3D coral models imaged in Curaçao: George, Mullinix, et al PeerJ 2021
Open the record for dataset details and reuse information.
Segmentations of 3D electron microscopy image volume from an albino mouse dorsal lateral geniculate nucleus
Open the record for dataset details and reuse information.
CLIC Calorimeter 3D images: Photon showers at Random Angle
<p>Energy deposits from single-particle showers in the ECAL+HCAL calorimeters of the CLIC detector</p> <p>Simulation performed with GEANT4 (https://geant4.web.cern.ch) and DD4HEP software (https://dd4hep.web.cern.ch/dd4hep/)</p> <p>Photons entering the detector at variable energy and direction</p> <p>See https://arxiv.org/abs/1912.06794 for details</p>
Fig. 3.2 in Handbook of best practice and standards for 2D+ and 3D imaging of natural history collections
Fig. 3.2. Camera positions of a single rotation when taking pictures of an object.
Fig. 4.1 in Handbook of best practice and standards for 2D+ and 3D imaging of natural history collections
Fig. 4.1. Scorpion pictured in UV fluorescence. Focus stacking image.
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.