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250 results for “3D analysis”
7 Year Follow up Analysis on the Speed of Progression of Tooth Wear Using 3D Subtraction
ClinicalTrials.gov study NCT04790110. IPD Sharing: NO. Countries: 1. Publications: 3.
Allograft Ridge Augmentation: 3D Analysis of CAD/CAM Custom Milled and Prefabricated Conventional Allogeneic Bone Blocks and Dental Implant Follow-up
ClinicalTrials.gov study NCT06027710. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: The effects of aging on neuropil structure in mouse somatosensory cortex—A 3D electron microscopy analysis of layer 1
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Morphometric analysis of retinal ganglionic cells (3D confocal images) analyzed using filament tracer from Imaris software
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fMRI/fPACT 3D image stacks and analysis codes for function
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Data from: Use of anisotropy, 3D segmented atlas, and computational analysis to identify gray matter subcortical lesions common to concussive injury from different sites on the cortex
Traumatic brain injury (TBI) can occur anywhere along the cortical mantel. While the cortical contusions may be random and disparate in their locations, the clinical outcomes are often similar and difficult to explain. Thus a question that arises is, do concussions at different sites on the cortex affect similar subcortical brain regions? To address this question we used a fluid percussion model to concuss the right caudal or rostral cortices in rats. Five days later, diffusion tensor MRI data were acquired for indices of anisotropy (IA) for use in a novel method of analysis to detect changes in gray matter microarchitecture. IA values from over 20,000 voxels were registered into a 3D segmented, annotated rat atlas covering 150 brain areas. Comparisons between left and right hemispheres revealed a small population of subcortical sites with altered IA values. Rostral and caudal concussions were of striking similarity in the impacted subcortical locations, particularly the central nucleus of the amygdala, laterodorsal thalamus, and hippocampal complex. Subsequent immunohistochemical analysis of these sites showed significant neuroinflammation. This study presents three significant findings that advance our understanding and evaluation of TBI: 1) the introduction of a new method to identify highly localized disturbances in discrete gray matter, subcortical brain nuclei without postmortem histology, 2) the use of this method to demonstrate that separate injuries to the rostral and caudal cortex produce the same subcortical, disturbances, and 3) the central nucleus of the amygdala, critical in the regulation of emotion, is vulnerable to concussion.
Data from: A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture
A prerequisite for the systems biology analysis of tissues is an accurate digital three-dimensional reconstruction of tissue structure based on images of markers covering multiple scales. Here, we designed a flexible pipeline for the multi-scale reconstruction and quantitative morphological analysis of tissue architecture from microscopy images. Our pipeline includes newly developed algorithms that address specific challenges of thick dense tissue reconstruction. Our implementation allows for a flexible workflow, scalable to high-throughput analysis and applicable to various mammalian tissues. We applied it to the analysis of liver tissue and extracted quantitative parameters of sinusoids, bile canaliculi and cell shapes, recognizing different liver cell types with high accuracy. Using our platform, we uncovered an unexpected zonation pattern of hepatocytes with different size, nuclei and DNA content, thus revealing new features of liver tissue organization. The pipeline also proved effective to analyse lung and kidney tissue, demonstrating its generality and robustness.
Data from: Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis
<p>Mammalian sex is determined by opposing networks of ovarian and testicular genes that are well characterized. However, its epigenetic regulation is still largely unknown, thus limiting our understanding of a fundamental process for species propagation. Here we explore the 3D chromatin landscape of sex determination <em>in vivo</em>, using <em>METALoci</em>, a novel genome spatial auto-correlation analysis.</p> <p><strong>Extended Data File 1: Coordinates for HH metaloci in each sample.</strong></p> <p>The EDFile1_H3K27ac_HH_metaloci_per_gene.zip file contains four files named:</p> <ul> <li>XX10.5_H3K27ac_HH_metaloci_per_gene.bed</li> <li>XX13.5_H3K27ac_HH_metaloci_per_gene.bed</li> <li>XY10.5_H3K27ac_HH_metaloci_per_gene.bed</li> <li>XY13.5_H3K27ac_HH_metaloci_per_gene.bed</li> </ul> <p>Each BED file contains the following columns tab separated:</p> <ul> <li>chr Chromosome</li> <li>start Start coordinates</li> <li>end End coordinates</li> <li>MetaLociBinNumber Number of the bin in the METALoci layout</li> <li>GeneSymbol Gene symbol</li> </ul> <p> </p> <p><strong>Extended Data File 2: Coordinates bins in METALoci with ATAC-seq accessible peak targeted by TF.</strong></p> <p>The EDFile2_TF_ATAC_ML_Sites.zip file contains four files named:</p> <ul> <li>XX10.5_TF_ATAC_ML_Sites.tsv</li> <li>XX13.5_TF_ATAC_ML_Sites.tsv</li> <li>XY10.5_TF_ATAC_ML_Sites.tsv</li> <li>XY13.5_TF_ATAC_ML_Sites.tsv</li> </ul> <p>Each TSV file contains the following columns tab separated:</p> <ul> <li>chr Motif site chromosome </li> <li>start Motif site start coordinates </li> <li>end Motif site end coordinates</li> <li>bin Hi-C bin number</li> <li>pchr ATAC site chromosome</li> <li>pstart ATAC site start coordinates</li> <li>pend ATAC site end coordinates</li> <li>gene Gene symbol</li> </ul>
Federated learning dataset: A case study of vibration analysis for desktop 3D printers
<p>This dataset contains the acceleration data collected from six low-cost 3D printers (same make and model) air-printing cubes with different printing speeds. This dataset can be used as a case study for federated learning, personalized learning, etc.</p>
Figures 31-33 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 31-33 Quasicalathus, light microscopic images of the holotypes of Q. agonicollis sp. nov. (31.) and Q. conservans sp. nov. (32, 33.). 31. Ventral side of head showing chaetotaxy of mentum; 32. General view of the amber piece with fossil in dorsal view; 32. Left lateral view. Abbreviations: ce – compound eye; el – elytron; ems – external seta of submentum; gu – gula; ims – internal seta of submentum; msf – mesofemur; mt – mentum; mtf – metafemur; prf – profemur; pt – pronotum.
Figures 47-51 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 47-51 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimen "Groehn 7889". 47. Dorsal aspect; 48. Left lateral aspect; 49. Ventral aspect; 50. Pronotum (the arrows point to the insertions of the lateral setae); 51. Prosternum (for better view the prolegs are partly removed using the clipping plane function of Amira software. Abbreviations: cx – procoxa; psp – prosternal process; tr – protrochanter.
Figures 6-12 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 6-12 Quasicalathus elpis (Ortuño and Arillo 2009), light microscopic images of specimens "Groehn 7889" (6–8.) and "Groehn 7962" (9–12.). 6, 10. General view of the amber pieces (in Fig. 6, only the part of the large amber piece bearing the Quasicalathus fossil is shown); 7. Ventral side of body; 8. Left mesotarsi iv + v; 9. Pronotum and anterior part of elytra, left side of body; 11, 12. Medial part of left elytron (Fig. 12 shows the enlarged part of the elytron marked by the white frame in Fig. 11; the white arrow points to the insertion of the discal seta). Abbreviations: bs – insertion of the pronotal laterobasal seta; hm – humerus; I–VIII – elytral intervals 1–8.
Figures 34-38 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 34-38 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimens "Groehn 4879" (34–37.) and "Groehn 7814" (38.). 34. Dorsal aspect; 35. Right lateral aspect; 36. Ventral aspect; 37, 38. Prosternum and basal portions of prolegs. Abbreviations: cx – procoxa; fm – profemur; psp – prosternal process; tr – protrochanter.
Figures 81-89 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 81-89 Quasicalathus conservans sp. nov., volume rendering of the holotype. 81. Head, dorsal aspect (the arrows point to the insertions of the supraorbital setae); 82. Head, ventral aspect; 83. Left external part of metathorax, ventral view; 84. Submentum (the arrows point to the insertions of the four lateral setae); 85. Posterior part of prosternum and procoxae; 86. Posterior part of metasternum and metacoxae; 87–89. Preserved remains of the aedeagus (87. Right lateral aspect; 88. Dorsal aspect; 89. Left lateral aspect). Abbreviations: bb – basal bulb of aedeagal median lobe; ce – compound eye; cxp – metacoxal plate; eph – partly evaginated lobes of endophallus; gu – gula; mem – metepimeron; mes – metepisternum; mtt – mentum tooth; mv – metaventrite; pcx – procoxa; pmr –preserved distal part of right paramere of aedeagal median lobe; psp – prosternal process; sc – scutellum; sps – setae of sensory pit; tl – terminal lamella of aedeagal median lobe.
Figures 61-64 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 61-64 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimens "MAIG 76" (61–63.) and "GZG 16185" (64.); 61. Dorsal aspect; 62. Right lateral aspect; 63, 64. Pronotum (the pronotal outline on left side is highlighted by dotted line in Fig. 64).
Figures 39-46 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 39-46 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimen "Groehn 7814" using different grey scales of the Amira software. 39. Dorsal aspect; 40. Lateral aspect. The displaced aedeagus (highlighted by red colour) was separated by the segmentation function of Amira software in Figures 39 and 40; 41. Head (the arrows point to the insertions of the supraorbital setae); 42. Pronotum (the arrows point to the insertions of the lateral setae); 43–46. Remains of the aedeagus in right lateral aspect (43.); Left lateral aspect (44.); Left lateral aspect (45.); Dorsal aspect (46.). The distal margins of the styloid apophysis of the right paramere in Fig. 43 and the lobate apophysis of the left paramere in Fig. 45 are highlighted by red dotted lines. Abbreviations: bb – basal bulb of aedeagal median lobe; os – distal ostium; pml – left paramere; pmr – right paramere; tl – terminal lamella of median lobe.
Figures 78-80 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 78-80 Quasicalathus conservans sp. nov., volume rendering of the holotype using different grey scales of the Amira software. 78. Dorsal aspect; 79. Left lateral aspect (aed – aedeagus); 80. Ventral aspect; the aedeagus (highlighted by red colour) was separated by the segmentation function of Amira software.
Figures 52-57 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 52-57 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimen "Groehn 7889". 52. Head, ventral aspect (the arrows point to the insertions of the setae near base of mentum tooth and on submentum); 53. Abdomen, left lateral aspect (the arrows point to the insertions of the setae on ventrites IV, V, and VI); 54. Metacoxal area (the arrows point to the insertions of the coxal setae); 55. Apical gonocoxites, ventral aspect; 56. Apical gonocoxites, dorsal aspect; 57. Gonocoxites and remains of the bursa copulatrix (the latter was highlighted by red colour using the segmentation function of Amira software). Abbreviations: at – apical tooth of retinacle; kes – metathoracic katepisternum; cx – metacoxa; cxp – metacoxal plate; des – dorsal ensiform setae; ep – elytral epipleuron; fm – metafemur; gu – gula; mdl – left mandible; gx1 – basal gonocoxite; gx2 – apical gonocoxite; mdr – right mandible; mo – molar; mt – mentum; sp – sensory pit; tr – metatrochanter; ves – ventral ensiform setae; v3, v4, v5, v6 – ventritres III, IV, V, VI.
Figures 73-77 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 73-77 Quasicalathus agonicollis sp. nov., volume rendering of specimen "GZG 16188". 73. Dorsal aspect; 74. Basal portion of pronotum and anterior part of elytra (right side of body; the arrows point to the insertions of the pronotal basolateral seta and the parascutellar seta); 75. Prosternum with basal portion of prolegs; 76. Left apical gonocoxite, ventral aspect; 77. Gonocoxites, ventral aspect. Abbreviations: cx – procoxa; des – dorsal ensiform setae; fm – profemur; gx1 – basal gonocoxite; gx2 – apical gonocoxite; hm – humerus; pst – prosternum; sc – scutellum; sps – setae of sensory pit; tr – protrochanter; ves – ventral ensiform setae.
Figures 13-17 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 13-17 Quasicalathus elpis (Ortuño and Arillo 2009), light microscopic images of specimens "CCHH 952" (13–15.) and "OSAC 269" (16, 17.). 13. Dorsal view of body; 14. Pronotum and anterior part of elytra showing the markedly concave basal margin and projected humeri (the white arrows point the insertion pores of the parascutellary setae); 15, 17. General view of the amber pieces; 16. Posterior part of left elytron (the white arrow points to the insertion of the discal seta).
ScienceDex guides
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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.