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438 results for “3D imaging”
3D in situ imaging of egg and larval dispersal from a Nassau Grouper spawning aggregation off Little Cayman, Cayman Islands
<p>Over multiple years, we released drifters into egg plumes from the large Nassau Grouper spawning aggregation off the west end of Little Cayman, Cayman Islands. For two cohorts spawned in 2017, we used an in situ plankton imaging system mounted to an undulating towed vehicle to observe the 3D positions of individual eggs and larvae around the drifters up to 36 hours after spawning. We used these data to estimate parameters of a 3D diffusion-mortality model and then predicted the concentration of eggs and larvae around previous years’ drifter tracks to evaluate the possibility of retention and export to nearby islands within five days of spawning. These show local retention on spawning nights in 2017 and 2011, a key year when a large cohort was spawned that subsequently drove population recovery.</p>
Datasets for 3D shape reconstruction from 2D microscopy images
<p>Here we publish two single cell datasets for 3D shape reconstruction from 2D microscopy images with a detailed description.</p>
In Situ Volumetric Imaging and Analysis of FRESH 3D Bioprinted Constructs Using Optical Coherence Tomography (Data and 3D models)
<p>These files contain 3D models and reconstructions of the 3D printed models after OCT imaging of the brain stem, circle of willis, kidney, vestibular apparatus, mixing network, and resolution text. These are from the journal article "In Situ Volumetric Imaging and Analysis of FRESH 3D Bioprinted Constructs Using Optical Coherence Tomography" published in <em>Biofabrication </em>(2022).</p>
SNEMI3D: 3D Segmentation of neurites in EM images
<p>In this challenge, a full stack of electron microscopy (EM) slices will be used to train <strong>machine-learning algorithms</strong> for the purpose of <strong>automatic</strong> <strong>segmentation of neurites in 3D</strong>. This imaging technique visualizes the resulting volumes in a highly anisotropic way, i.e., the x- and y-directions have a high resolution, whereas the z-direction has a low resolution, primarily dependent on the precision of serial cutting. EM produces the images as a projection of the whole section, so some of the neural membranes that are not orthogonal to a cutting plane can appear very blurred. None of these problems led to major difficulties in the manual labeling of each neurite in the image stack by an expert human neuro-anatomist.</p> <p>In order to gauge the current state-of-the-art in automated neurite segmentation on EM and compare between different methods, we are organizing a 3D Segmentation of neurites in EM images (SNEMI3D) challenge in conjunction with the<a href="http://www.biomedicalimaging.org/2013/program/isbi-challenges/"> ISBI 2013 conference</a>. For this purpose, we are making available a large training dataset of mouse cortex in which the neurites have been manually delineated. In addition, we also provide a test dataset where the 3D labels are not available. The aim of the challenge is to compare and rank the different competing methods based on their<strong> object classification accuracy</strong> in three dimensions.</p> <p>The <strong>image data</strong> used in the challenge was produced by <a href="http://lichtmanlab.fas.harvard.edu/">Lichtman Lab at Harvard University</a> (Daniel R. Berger, Richard Schalek, Narayanan "Bobby" Kasthuri, Juan-Carlos Tapia, Kenneth Hayworth, Jeff W. Lichtman) and manually annotated by <a href="http://lichtmanlab.fas.harvard.edu/people/daniel-berger">Daniel R. Berger</a>. Their corresponding biological findings were published in <a href="http://www.ncbi.nlm.nih.gov/pubmed/26232230">Cell (2015)</a>.</p>
FIGURE 15. NOvOcrania philippinensis ventral valve and 3D images. A. ZMB Bra 2409 in A review of all Recent species in the genus Novocrania (Craniata, Brachiopoda)
FIGURE 15. NOvOcrania philippinensis ventral valve and 3D images. A. ZMB Bra 2409 (Taiwan). Ventral valve interior with rostellum, tubercles on margin and deeply incised mantle canals. B, D, E. OU 44518b (Vancouver Island, Canada). B. Partial ventral valve interior. D. 3D image from micro-CT scan, oblique cutaway through whole specimen (line D on Fig. 15B) showing slightly raised support structure scar and small mound on dorsal valve (where small anterior muscles attach) and calcitic rostellum on ventral valve. E. Vertical slice from micro-CT scan down midline (line E on Fig. 15B) showing a small mound on dorsal valve and rostellum on ventral valve. C. IGSP 58850 (Sado Island, Japan). Ventral valve interior.
Yutu-2 PCAM Images for 3D Scene Reconstruction (2020)
<p>Here's the image data from Chang'e-4's Yutu-2 panoramic camera (PCAM) in 2020, with 3D scene reconstruction.<br>There are also 2831 impact craters, ranging from 0.1 metres to 5.93 metres in diameter.<br>All impact craters are categorised into five degradation classes (A, AB, B, BC, C).</p>
Yutu-2 PCAM Images for 3D Scene Reconstruction (2019)
<p>Here's the image data from Chang'e-4's Yutu-2 panoramic camera (PCAM) in 2019, with 3D scene reconstruction.<br>There are also 4625 impact craters, ranging from 0.1 metres to 6.37 metres in diameter.<br>All impact craters are categorised into five degradation classes (A, AB, B, BC, C).</p>
Yutu-2 PCAM Images for 3D Scene Reconstruction (2021)
<p>Here's the image data from Chang'e-4's Yutu-2 panoramic camera (PCAM) in 2021, with 3D scene reconstruction.<br>There are also 4525 impact craters, ranging from 0.1metres to 5.86 metres in diameter.<br>All impact craters are categorised into five degradation classes (A, AB, B, BC, C).</p>
3D lithium-ion battery image for testing P3T-Net
<p>These are the dataset used for training and testing P3T-Net for 3D unpaired domain transfer in .tif format. Images can be directly opened with ImageJ, Avizo, Python, Matlab, etc.</p> <p>Target domain: nano-CT image of a dual-mode scan of Lithium-ion battery cathode (voxel size: 128nm); Source domain: a nano-CT images of a single-mode scan of lithium-ion battery cathode (voxel size: 128nm).</p>
Hyperspectral Oblique Plane Microscopy -- microparticles 3D & laser beam profile & hyperspectral image of UV adhesive
<p>Processed spectra data for microparticle classification and raw hyperspectral images from mixture of microparticle</p>
Supplementary material 2 from: Ströbel B, Schmelzle S, Blüthgen N, Heethoff M (2018) An automated device for the digitization and 3D modelling of insects, combining extended-depth-of-field and all-side multi-view imaging. ZooKeys 759: 1-27. https://doi.org/10.3897/zookeys.759.24584
SV1: EDOF imaging : Explanation note: This video demonstrates the effect of the registered EDOF-calculation.
Supplementary material 1 from: Ströbel B, Schmelzle S, Blüthgen N, Heethoff M (2018) An automated device for the digitization and 3D modelling of insects, combining extended-depth-of-field and all-side multi-view imaging. ZooKeys 759: 1-27. https://doi.org/10.3897/zookeys.759.24584
Technical information : Explanation note: Detailed technical information and additional theoretical background.
Supplementary material 3 from: Ströbel B, Schmelzle S, Blüthgen N, Heethoff M (2018) An automated device for the digitization and 3D modelling of insects, combining extended-depth-of-field and all-side multi-view imaging. ZooKeys 759: 1-27. https://doi.org/10.3897/zookeys.759.24584
SV2: Illustrative examples : Explanation note: Illustrative examples of insects and snail shell models generated with DISC3D.
FIGURE 5. Micro-computed tomography 3D images. A–D in A new species of sponge crab of the genus Epigodromia McLay 1993 (Crustacea: Brachyura: Dromiidae) from the southeastern Arabian Sea, with notes on the Zoogeography
FIGURE 5. Micro-computed tomography 3D images. A–D, dorsal view; B–C, frontal view with chelipeds outer view. A, B, Epigodromia mclayi sp. nov., holotype, male (cw 11.43 mm, cl 10.33 mm), (IO/SS/BRC00370), southeastern Arabian Sea, Tamil Nadu, India; C–D, Epigodromia gilesii Alcock, 1900, male (cw 5.8 mm, cl 6.05 mm), (IO/SS/BRC00372), Malabar coast, southeastern Arabian Sea, India.
DIC Images and Data of In-Plane Cyclic Testing of a 3D-Woven Layer-to-Layer Angle Interlock Composite
<p>Data behind the publications:</p> <ul> <li>C. Oddy, M. Song, C. Stewart, B. El Said, M. Ekh, S. Hallett and Martin Fagerström: On and Off-Axis Cyclic Behaviour of 3D-Woven Composites: Experimental Testing and Macroscale Modelling. Submitted for international publication.</li> </ul> <p>For each test sample orientation and excel file is provided. This includes the machinedata giving the time, machine displacement and force. On another sheet, informationfrom the DIC analysis is given, including the time and force signal organised accordingto the image frame number. The DIC images are also provided.</p> <p>The testing was carried out using a serial camera DIC system. However, as part of this publication, the images have only been provided from one of the camera systems. They have also been exported at a lower image quality than the original analysis. The authors' can recommend the use of open source DIC software, for example DICe (https://github.com/dicengine/dice), to carry out any type of further image processing. Processing the stereo image as a 2D analysis at a lower image quality may lead to some deviations in the extracted strain or displacement fields. The authors however have compared the results and have not seen any notable inconsistencies. We hope that these images can be useful to you in your own research endeavours! </p> <p> </p>
3D images of a turtle embryo
<p>Turtle eggs containing embryos are exceedingly rare in the fossil record. Here, we provide the first description and taxonomic identification, to our knowledge, of a fossilized embryonic turtle preserved in an egg, a fossil recovered from the Upper Cretaceous Xiaguan Formation of Henan Province, China. Through Computed Tomography and Three-Dimensional reconstruction, many bones can be clearly displayed, including the maxillae, mandibles, ribs, plastral plates, scapula, forelimbs, and hind limbs. The specimen is attributed to the Nanhsiungchelyidae (Pan-Trionychia), an extinct group of large terrestrial turtles (possibly the species <i>Yuchelys nanyangensis</i>). The egg is rigid, spherical, and is one of the largest and thickest shelled Mesozoic turtle eggs known. Importantly, this specimen allowed identification of other nanhsiungchelyid egg clutches and comparison to those of Adocidae, as Nanhsiungchelyidae and Adocidae form the basal extinct clade Adocusia of the Pan-Trionychia (includes living soft-shelled turtles). Despite the differences in habitat adaptations, nanhsiungchelyids (terrestrial) and adocids (aquatic) shared several reproductive traits, including relatively thick eggshells, medium size clutches and relatively large eggs, which may be primitive for trionychoids (including Adocusia and Carrettochelyidae). The unusually thick calcareous eggshell of nanhsiungchelyids compared to those of all other turtles (including adocids) may be related to a nesting style adaptation to an extremely harsh environment.</p>
3D Interferometric Lattice Light-Sheet Imaging
<p>This repository contains experimental data and code supporting the publication: Cao <em>et al.</em>, Volumetric Interferometric Lattice Light Sheet Imaging.<strong><em>Nat. Biotechnol. </em></strong>(2021), DOI: https://doi.org/10.1038/s41587-021-01042-y</p> <p>Details about the files are provided in the Readme files in the associated sub-folders.</p> <p>3D-iLLS setup photos can be found in https://github.com/PertsinidisLab/3D-iLLS-photos</p>
Hypocenter-based 3D Imaging of Active Faults: Method and Applications in the Southwestern Swiss Alps [Dataset]
<p>Data repository to the JGR publication of Truttmann et al. (2023), including following datasets for the two analyzed earthquake sequences (St. Léonard and Anzère)</p> <p>- Interactive 3D fault-network models</p> <p>- Focal mechanisms</p> <p>- Relocated hypocenter locations (hypoDD)</p> <p>- Station networks</p> <p>- hypoDD parameters</p>
Supplementary movies and datasets of the paper: Precise targeting for 3D cryo-correlative light and electron microscopy volume imaging of tissues using a FinderTOP
<p>Imaging data supporting the paper: </p> <p>Precise targeting for 3D cryo-correlative light and electron microscopy volume imaging of tissues using a FinderTOP, containing raw and processed data from fluorescent and electron microscopy.</p> <p> </p>
Data for: Contributions of deep learning to automated numerical modelling of the interaction of electric fields and cartilage tissue based on 3D images
<p>Replication data for: Contributions of deep learning to automated numerical modelling of the interaction of electric fields and cartilage tissue based on 3D images</p> <p> </p> <p> </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.