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60 results for “3D morphology”
MRI Neonatal Lung Segmentation and 3D Morphologic Features
<p>We developed an ensemble of deep convolutional neural networks (2D-UNets) to perform automated neonatal lung segmentation from MRI sequences. A three-dimensional reconstruction is used to calculate MRI features for lung volume, shape, pixel intensity, and surface.</p> <p>In addition, ML Models for severity prediction of Bronchopulmonary Dysplasia (BPD) are implemented as an applied example of the use of MRI lung volumetric features for disease prognosis.</p> <p>This dataset comprises:</p> <ul> <li>Three pretrained 2D-UNet Models for Neonatal MRI Lung Segmentation.</li> <li>Resulting performances and features per MRI-sequence.</li> </ul> <p>See Publication:</p> <p>Automated MRI Lung Segmentation and 3D Morphologic Features for Quantification of Neonatal Lung Disease (2023)</p> <p><a href="https://doi.org/10.1148/ryai.220239">https://doi.org/10.1148/ryai.220239</a></p>
Supplementary Information and Data for "Unveiling the 3D Morphology of Epitaxial GaAs/AlGaAs Quantum Dots"
<p>Raw and processed TEM and AFM data for the article <strong><em>Unveiling the 3D Morphology of Epitaxial GaAs/AlGaAs Quantum Dots</em></strong>.</p> <p>Paper: <a href="https://doi.org/10.1021/acs.nanolett.4c02182" target="_blank" rel="noopener">https://doi.org/10.1021/acs.nanolett.4c02182</a></p> <p>Preprint: <a href="https://arxiv.org/abs/2405.16073" target="_blank" rel="noopener">https://arxiv.org/abs/2405.16073</a></p> <p>The TEM data has a PDF information file included with description of the file types and how to open them.</p> <p>The AFM Nanosurf .nid files can be opened, e.g., with <a href="http://gwyddion.net/" target="_blank" rel="noopener">Gwyddion</a>.</p>
Supplementary data for the journal article "Quantifying the impact of 3D pore space morphology on diffusive mass transport in loam and sand"
<p>Binarized cutouts (black=pore, white=soil) of 3D CT images of soil samples from loam and sand together with geometrical descriptors and diffusive properties computed on these cutouts. The geometrical descriptors include, among others, porosity, specific surface area, geodesic tortuosity, geometric tortuosity, constrictivity, mean chord length and mean of spherical contact distribution. Diffusion is quantified by the so-called M-factor which equals the ratio of the effective and intrinsic diffusivity.</p> <p>This data supplements the journal article "Quantifying the impact of 3D pore space morphology on diffusive mass transport in loam and sand". Additional information can be found there.</p>
Fig. 12 3D in On Roth's "human fossil" from Baradero, Buenos Aires Province, Argentina: morphological and genetic analysis
Fig. 12 3D models produced from the CT-scans of the 19 skull bone fragments. See Table 2 for references on which bones are contained in each fragment. Since fragments 17 and 18 did not present any diagnostic features, it was not possible to identify them and were not employed in the reconstruction
FIGURE 2. 3D in The inner morphology of the petrosal bone of the endemic elephant of Tilos Island, Greece
FIGURE 2. 3D reconstruction of the petrosals, samples (A-C) T2406 along with transparent views locating the orientation of the labyrinth in the bone, (D-F) T2506 and (G-I) T137. A, D, G ventrolateral view; B, E, H dorsolateral view; C, F, I dorsomedial view. See text for abbreviations.
Figure 4. The 3D in Morphological variation of pumpkinseed (Lepomis gibbosus) with emphasis on allometry
Figure 4. The 3D plot of first three principal components with five times exaggerated deformation grids along principal components (deformation grid on the left illustrates the negative side of the axis, whereas right illustration is the positive side of the axis.)
Figure 9. Schematic 3D in Morphology and spatial constraints in a dorso-ventrally flattened skull, with a revised species description of Platyallabes tihoni (Poll, 1944)
Figure 9. Schematic 3D reconstruction of the lower jaw-suspensorium articulation area. (a) Overview of the lower jaw, suspensorium and part of skull at level of articulation with suspensorium. Solid lower jaw indicates closed mouth, transparent lower jaw indicates open mouth. Black arrow shows displacement of lower jaw according to the black axis indicated at the jaw articulation. The grey arrows indicate the movements of the lower jaw halves if they were rotated along the grey axis at the articulation. (b) Detail from a postero-ventral view of the lower jaw articulation, showing the two rotation axis: black rod represents the axis which allows a proper mouth opening, grey rod represents the axis of rotation which has shifted together with the suspensorium. Rotation along the black axis results in the medial position of the retroarticular process; with respect to the suspensorium (transparent lower jaw indicates the closed mouth, solid lower jaw the open mouth).
FIG. 31. Digital 3D in Cranial Morphology And Phylogenetic Relationships Of Trigonostylops Wortmani, An Eocene South American Native Ungulate
FIG. 31. Digital 3D reconstructions of left osseous labyrinths of Trigonostylops wortmani AMNH VP-28700 and Astrapotherium magnum MACN A 3208 in lateral, ventral, and dorsal views. Both specimens are damaged (area of fenestra vestibuli in AMNH VP-28700; fenestra cochleae in MACN A 3208: arrow).
DEM, rock point clouds, and 3D morphological features of Martian rocks in the landing region of Zhurong rover
<p>Rocks on the Martian surface and their three-dimensional (3D) morphology record the geological evolution of Mars and its interaction history with outer space. China's Zhurong Mars rover has traveled on Mars for nearly 2 kilometers and obtained a wealth of data, enabling the fine-scale measurement and morphological analysis of 3D Martian rocks. With 178 high-resolution Zhurong NaTeCams stereo images acquired in rings covering large circular areas, we extracted 6,185 3D rocks from centimeter-scale to meter-scale distributed along the traverse of the Zhurong rover using an automatic approach. This dataset includes the digital elevation model (DEM), extracted rocks in point clouds, and the 3D morphological features of rocks derived from the Zhurong NaTeCams images, obtained in six areas along the traverse of the Zhurong rover.</p> <p>To use this dataset, please cite "Li, Y., Xiao, Z., Ma, C., Zeng, L., Zhang, W., Peng, M., & Li, A. (2023). Extraction and Analysis of Three‐dimensional Morphological Features of Centimeter‐scale Rocks in Zhurong Landing Region. <em>Journal of Geophysical Research: Planets</em>, e2022JE007656."</p>
Prediction of Diblock Copolymer Lamellar Morphologies in 3D and Complex Geometry via Machine Learning
<p>3d morphology evolution of diblock copolymer via 3D UNet.</p> <p>Manuscript: Prediction of Diblock Copolymer Lamellar Morphologies in 3D and Complex Geometry via Machine Learning</p>
FIG. 15. — 3D in A sabre-tooth predator from the Neotropics: Cranial morphology of Anachlysictis gracilis Goin, 1997 (Metatheria, Thylacosmilidae), based on new specimens from La Venta (Middle Miocene, Colombia)
FIG. 15. — 3D digital models of the skull of Anachlysictis gracilis Goin, 1997, based on the specimen VPPLT 1612. Original 3D scans of the skull in lateral (A) and anterior (B) views; modified retrodeformed skull with original unmodified mandible, in lateral (C) and anterior (D) views. Scale bar: 20 mm.
Data from: 3D morphology of an outer-hair-cell hair bundle increases its displacement and dynamic range
Open the record for dataset details and reuse information.
3D representation of meso-voids location and morphology within the fibrous pore space of three carbon fabrics
<p>Segmented meso-voids from a tomography scan of preforms impregnated under capillary dominated conditions, combined to 3D scans of the initial prefrom dry state.</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: 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.
FIGURE 6. 3D in Confocal laser scanning microscopy technique for the study of internal genitalia and external morphology of eriophyoid mites (Acari: Eriophyoidea)
FIGURE 6. 3D-reconstruction of the internal genitalia of Phytoptus rigidus, bottom view (the same female as Fig. 2A). A. spermathecae, B. spherical spermathecal tube, C. capsule-like reservoir in the connection of two spermathecal tubes, D. transversal genital apodeme, E. distal folder of transversal genital apodeme, F. longitudinal genital? apodeme1 (includes two sclerotised plates), G. epigynium.
Dataset of PNAS article "Morphological instability and roughening of growing 3D bacterial colonies"
<p>Dataset of the PNAS article "Morphological instability and roughening of growing 3D bacterial colonies", including numerical simulations and raw images of all Main Text and SI figures.</p>
FIGURE 8. 3D in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 8. 3D volume renderings of O. margoi using the micro-CT technology. Contrast enhancement to expose the denser parts. A, dorsal view of the whole body until the posterior sucker (ps) enouncing the digestive system. From the posterior intestine (pi) two lateral post ceca are starting (pca). Four pairs of blind ending lateral diverticula (ld) are diverting from the posterior intestine that finally enlarge to form a sac-like structure. Arrows indicate the two lateral blind-ended sacks in the last sack of the posterior intestine. B, frontal view of the anterior sucker (as) showing the four lines of lateral columnar glands (gl) and a central gland-like structure separated from the other (arrow). Scale bar = 1mm.
Fig. 4 3D in The cephalic morphology of free-living and cave-dwelling species of trechine ground beetles from China (Coleoptera, Carabidae)
Fig. 4 3D reconstructions of antennal muscles of S. wangorum (a) and T. perroti (b) and labial muscles of S. wangorum (c) and T. perroti (d). Upper part of each image: dorsal view; lower part of each image: ventral view. ata anterior tentorial arm, dta dorsal tentorial arm, gur gular ridge, mt mentum, pg palpiger
Fig. 2 3D in The cephalic morphology of free-living and cave-dwelling species of trechine ground beetles from China (Coleoptera, Carabidae)
Fig. 2 3D reconstructions of tentoriums (a, b, c) and nervous + digestive systems (d, e, f). a, d S. wangorum. b, e T. perroti. c, f B. sp. Upper part of each image: dorsal view; lower part of each image: ventral view. ata anterior tentorial arm, cer cerebrum, cn connective, dta dorsal tentorial arm, fg frontal ganglion, gur gular ridge, p pharynx, tb tentorial bridge
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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.