Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
46
datasets available to search
ShareScore release 0.9.0
Dataset results
46 results for “3D human models”
3D Models and Silhouettes for Human Body Reshape with DL from the ANSUR Dataset
<p><strong>Citations</strong><br><br>If you use this dataset in your research, please cite the original paper: </p> <p>Curbelo, J.P., Spiteri, R.J. A methodology for realistic human shape reconstruction from 2D images. Multimedia Tools and Applications (2024), <a href="https://doi.org/10.1007/s11042-023-17947-6">DOI: 10.1007/s11042-023-17947-6</a></p>
The human splenic microcirculation is entirely open as shown by 3D models in virtual reality. Supplementary files
<p>These materials supplement our paper "The human splenic microcirculation is entirely open as shown by 3D models in virtual reality".</p> <p><strong>Summary</strong></p> <p>The human spleen is equipped with an organ-specific microcirculation. The initial part of the venous circulation is formed by spleen-specific large microvessels, the sinuses. Sinuses eventually fuse to form venules and veins. For more than 170 years there have been debates, whether splenic red pulp capillaries join sinuses, i.e., whether the microcirculation is closed or open - or even simultaneously closed and open. We have now solved this question by three-dimensional reconstruction of a limited number of immunostained serial sections of red and white pulp areas, which were visualized in virtual reality. Splenic capillaries have special end structures exhibiting multiple small diverging endothelial cell processes, which always keep a certain distance to the walls of sinuses. Only very few capillary ends were difficult to diagnose. Positive identification of these end structures permits to conclude that the human splenic microcirculation is entirely open. This is also true for the perifollicular capillary network and for capillaries close to red pulp venules. Follicles are supplied by a relatively dense open perifollicular capillary net, which is primarily, but not exclusively, fed by sheathed and few non- sheathed capillaries from the surrounding red pulp network.</p> <p> </p> <p><strong>Interactive models</strong></p> <p>Each <em>file_sX.zip</em> contains a 3D model, registered sequence of serial sections (the input data to generate and validate the model), and an interactive / VR viewer. After you have unzipped the file, there are multiple batch files. Any of them can be used for an interactive model display on a normal monitor, but we recommend the file <em>start_index.bat</em>. Now, if you have a virtual reality headset or a 4K monitor, there are better options:</p> <ul> <li>If you have a HTC Vive-compatible headset (i.e., the "wand" controllers, typically coming with HTC Vive, Vive Pro, Vive Pro 2, etc.), please use <em>start_vive.bat</em>.</li> <li>If you have a Valve Index headset (i.e., the "knuckles" controllers, should also work with Oculus devices), please use <em>start_index.bat</em>.</li> <li>If you have a high-resolution monitor (4K or better), please use <em>start_interactive_4k.bat</em> for a high-resolution interactive model.</li> </ul> <p>In the zip-file is also a <em>README.txt</em> file with instructions on the controls for the interactive and VR viewer. It is also available in the viewer at press of F1 button. In a nutshell: </p> <ul> <li>ASWD control the movement</li> <li>I (the "i" key) turns the sections on and off</li> <li>JK advance the sections</li> <li>CV adjust the height</li> <li>E turns the model on and off.</li> </ul> <p>The viewer executables are built for Windows. They work with Windows 10, should work with previous versions of Windows (64 bit) and also with future versions, such as Windows 11. Users of other OS, such as MacOS or Linux, can use <a href="https://www.meshlab.net/">MeshLab</a> to look at the model. Any image viewer can be used to inspect the sections in the <em>img</em> folder of the unpacked zip file. However, in this case, no VR experience and no simultaneous view of both 3D reconstruction and the sections is possible.</p> <p> </p> <p><strong>Videos</strong></p> <p>The videos with the same content are mostly supplied in three versions:</p> <ul> <li>On any modern hardware you should be able to play the H.265 videos, ending in <em>...4K_h265_10bit.mov</em>, there are in 4K resolution</li> <li>If it is not the case, but you want 4K resolution, use the H.264 version, ending in <em>...4K_h264_10bit.mov,</em> it is also in 10 bit quality</li> <li>A fallback for weaker hardware and maximal compatibility is the H.264 FullHD version. It should play anywhere. Those files end in <em>...1080p_h264.mov.</em></li> </ul> <p> </p> <p><strong>Supplementary Figures S1 and S2</strong></p> <p>The supplementary figures with their legends are available in the file <a href="https://zenodo.org/record/6599487/files/supp.pdf"><em>supp.pdf</em></a>.</p> <p> </p> <p><strong>3D models corresponding to Figs. 4a-d</strong></p> <p><a href="https://zenodo.org/record/6599487/files/file_s1.zip?download=1">Supplementary file S1</a>. 3D model of ROI 1 with open capillary ends in red</p> <p><a href="https://zenodo.org/record/6599487/files/file_s2.zip?download=1">Supplementary file S2</a>. 3D model of ROI 2 with open capillary ends in red</p> <p><a href="https://zenodo.org/record/6599487/files/file_s3.zip?download=1">Supplementary file S3</a>. 3D model of ROI 3 with open capillary ends in red</p> <p><a href="https://zenodo.org/record/6599487/files/file_s4.zip?download=1">Supplementary file S4</a>. 3D model of ROI 4 with open capillary ends in red</p> <p> </p> <p><strong>File corresponding to Fig. 7a</strong></p> <p><a href="https://zenodo.org/record/6599487/files/file_s5.zip?download=1">Supplementary file S5</a>. 3D model of sinus network and open capillary ends in red</p> <p> </p> <p><strong>Files corresponding to Figs. 9a,b</strong></p> <p><a href="https://zenodo.org/record/6599487/files/file_s6.zip?download=1">Supplementary file S6</a>. 3D model of ROI 2 with perifollicular capillary network in red correspondig to Fig. 9a</p> <p><a href="https://zenodo.org/record/6599487/files/file_s7.zip?download=1">Supplementary file S7</a>. 3D model of ROI 2 with perifollicular capillary network in red and open ends in yellow corresponding to Fig. 9b</p> <p> </p> <p><strong>Videos corresponding to Figs 5a-f</strong></p> <p><a href="https://zenodo.org/record/6599487/files/sinus_-_video_s1_4K_h264_10bit.mov">Supplementary video S1</a>. Two capillaries with open ends in Fig. 5a-c</p> <p><a href="https://zenodo.org/record/6599487/files/sinus_-_video_s2_4K_h264_10bit.mov">Supplementary video S2</a>. Capillary with at least two open ends in Fig. 5d-f</p> <p> </p> <p><strong>Videos corresponding to Figs 6a-d</strong></p> <p><a href="https://zenodo.org/record/6599487/files/sinus_-_video_s3_1080p_h264.mov">Supplementary video S3</a>. Quality control of open ends shown in Fig. 5a-c and Fig. 6a,b</p> <p><a href="https://zenodo.org/record/6599487/files/sinus_-_video_s4_1080p_h264.mov">Supplementary video S4</a>. Quality control of open end shown in Fig 5d-f and Fig. 6c,d</p> <p> </p> <p><strong>Videos corresponding to Fig. 4d and Figs 8a-f</strong></p> <p><a href="https://zenodo.org/record/6599487/files/sinus_-_video_s5_1080p_h264.mov">Supplementary video S5</a>. Control of open capillary end shown in Fig. 8a-c</p> <p><a href="https://zenodo.org/record/6599487/files/sinus_-_video_s6_1080p_h264.mov">Supplementary video S6</a>. Control of open capillary end shown in Fig. 8d-f</p>
Parametric 3D CAD model of human foot
<p>The parametric 3D CAD model of human foot was developed from CT data. A CT (Toshiba® Aquilion 4 equipment) scan was performed on a 29 years old male (65 Kg). 345 slices were captured with a slice distance of 1.0 mm (see Figure 2.a). Scans were made for both feet in their neutral posture in which there is the least tension or pressure on tendons, muscles and bones. Medical images were, then, exported into standard .DICOM format (image resolution 512x512 pixels) and processed by using ScanIP® and SolidWorks.</p> <p>Bone structure was composed of 19 bones: tibia, fibula, talus, calcaneus, cuboid, navicular, 3 cuneiforms (bones of the metatarsus), 5 metatarsals (bones of the metatarsus) and 5 components of the phalanges (bones of the toes). Phalange bones (a proximal and a distal phalanx for the great toe; proximal, middle and distal phalanges for the second to fifth toes) were fused together since their relative motion do not affect plantar pressures.</p> <p>More details can be found in the publications below:</p> <ol> <li><strong>Franciosa, P.</strong>, Gerbino S., From CT Scan to Plantar Pressure Map Distribution of a 3D Anatomic Human Foot, in Proc. of COMSOL Conference’10, Paris (France), November 17-19, 2010.</li> <li><strong>Franciosa, P.</strong>, Gerbino, S., Lanzotti A., Silvestri L., Improving Comfort of Shoe Sole through Experiments based on CAD-FEM Modeling, Medical Engineering and Physics, doi:10.1016/j.medengphy.2012.03.007, 2013.</li> </ol>
Transcriptomic characterization of 2D and 3D human induced pluripotent stem cell-based in vitro models as New Approach Methodologies for developmental neurotoxicity testing
<p><strong>Abstract:</strong> The safety and developmental neurotoxicity (DNT) potential of chemicals remain critically understudied due to limitations of current in vivo testing guidelines, which are low throughput, resource-intensive, and hindered by species differences that limit their relevance to human health. To address these issues, robust new approach methodologies (NAMs) using deeply characterized cell models are essential. This study presents the comprehensive transcriptomic characterization of two advanced human-induced pluripotent stem cell (hiPSC)-derived models: a 2D adherent and a 3D neurosphere model of human neural progenitor cells (hiNPCs) differentiated up to 21 days. Using high-throughput RNA sequencing, we compared gene expression profiles of 2D and 3D models at three developmental stages (3, 14, and 21 days of differentiation). Both models exhibit maturation towards post-mitotic neurons, with the 3D model maturing faster and showing a higher prevalence of GABAergic neurons, while the 2D model is enriched with glutamatergic neurons. Both models demonstrate broad applicability domains, including excitatory and inhibitory neurons, astrocytes, and key endocrine and especially the understudied cholinergic receptors. Comparison with human fetal brain samples confirms their physiological relevance. This study provides novel in-depth applicability insights into the temporal and dimensional aspects of hiPSC-derived neural models for DNT testing. The complementary use of these two models is highlighted: the 2D model excels in synaptogenesis assessment, while the 3D model is particularly suited for neural network formation as observed as well in previous functional studies with these models. This research marks a significant advancement in developing human-relevant, high-throughput DNT assays for regulatory purposes.</p> <p><strong>This data sets contains:</strong></p> <p><strong>Tab. S1</strong> - Significant genes results</p> <p><strong>Tab. S2</strong> - Enriched pathways_GO_Biological Processes</p> <p><strong>Tab. S3</strong> - Enriched pathways_GO_Cellular Components</p> <p><strong>Tab. S4</strong> - Enriched pathways_GO_Molecular Function</p> <p><strong>Tab. S5</strong> - Enriched pathways_KEGG</p> <p><strong>Tab. S6</strong> - EnrichEnriched pathways_Panther</p> <p><strong>Tab. S7</strong> - Enriched pathways_Reactome</p> <p><strong>Tab. S8</strong> - Gene counts</p> <p><strong>Tab. S9</strong> - Gene selection for targeted analysis</p>
The OpenEar library of 3D models of the human temporal bone based on computed tomography and micro-slicing
<p>The OpenEar Dataset provides a library consisting of eight three-dimensional models of the human temporal bone to enable surgical training including color data. Each dataset is based on a combination of multimodal imaging including Cone Beam Computed Tomography (CBCT) and micro-slicing. 3D reconstruction of micro-slicing images and subsequent registration to CBCT images allowed for relatively efficient multimodal segmentation of inner ear compartments, middle ear bones, tympanic membrane, relevant nerve structures, blood vessels and the temporal bone. Raw data from the experiment as well as voxel data and triangulated models from the segmentation are provided in full for use in surgical simulators or any other application which relies on high quality models of the human temporal bone.</p>
A 3D multi-cellular tissue model of the human omentum to study mechanisms of ovarian cancer metastasis
<p>Here, the design of 3D multi-cellular tissue model of the human omentum is presented to study mechanisms of ovarian cancer metastasis.</p>
Towards safe human-to-robot handovers of unknown containers: pre-trained models and 3D hand keypoints annotations
<p>This repository contains additional data to be used with the implementation of the real-to-simulation framework of the paper <em>Towards safe human-to-robot handovers of unknown containers</em>. The data include pre-trained models and annotations of the 3D hand poses for selected recordings from the public training and testing sets of <a href="http://corsmal.eecs.qmul.ac.uk/containers_manip.html">CORSMAL Container Manipulation (CCM) dataset</a>. The pre-trained models are used for classifying the filling type and filling level of a container. 3D hand poses are annotated as 21 keypoints based on the <a href="https://github.com/CMU-Perceptual-Computing-Lab/openpose">OpenPose</a> format.</p>
3D model of the human ACE2 receptor bound to the SARS-CoV-2 Spike RBD
<p>3D structure model of the receptor-binding domain of SARS-CoV-2 (top) bound to the human ACE2 receptor (bottom). The two highlighted aminoacids - ACE2 D30 (red) and RBD K417 (blue) - are part of a set of interactions that is conserved in animal species susceptible to infection by the virus but are absent from immune species.</p>
TGF-beta dynamically controls epithelial identity in a 3D model of human epiblast [scRNAseq_HES3-MIXL1-GFP_hESC]
GEO Series GSE294585. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Modelling human pre-gastulation development by 3D culture of blastoids generated from the primed-to-naive transitioning intermediates [RNA-seq]
GEO Series GSE200933. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
TGF-beta dynamically controls epithelial identity in a 3D model of human epiblast [RNAseq_CRISPRi_ZNF398]
GEO Series GSE294448. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
A fully iPSC-derived 3D model of the human blood-brain barrier for exploring neurovascular disease mechanisms and therapeutic interventions
GEO Series GSE302761. Homo sapiens. 14 samples. Type: Expression profiling by high throughput sequencing.
Microglia-astrocyte interplay mitigates Aβ toxicity in a novel human 3D neurosphere model of Alzheimer’s Disease
GEO Series GSE272186. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
TGF-beta dynamically controls epithelial identity in a 3D model of human epiblast [scRNAseq]
GEO Series GSE294578. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Engineered 3D Immuno-Glial-Neurovascular Human miBrain Model
GEO Series GSE308670. Homo sapiens. 27 samples. Type: Expression profiling by high throughput sequencing.
TGF-beta dynamically controls epithelial identity in a 3D model of human epiblast [RNAseq_H9_KiPS]
GEO Series GSE294449. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Characterization of immortalized human lacrimal gland epithelial cells in 2D and 3D cell culture models
GEO Series GSE239464. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
Expression data from human 3D skin models treated with synthetic pseudo-ceramide for medical containing steroid cream
GEO Series GSE253780. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic analysis in human 3D skin model injected with resorbable hyaluronic acid fillers reveals foreign body response.
GEO Series GSE216279. Homo sapiens. 36 samples. Type: Expression profiling by array.
Transcriptome profile of Primary Human Lung Fibroblasts (Cystic Fibrosis vs. Non-Cystic Fibrosis) arranged in a 3D model of the connective airways tissue
GEO Series GSE141536. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
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.