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3,036 results for “ct”
Ferron Coal CT Scan
<p>CT scan of a Subbituminous Ferron Coal sample, cut at 1.5 diam x 3" length, obtained from underground mine in San Rafael Swell, Utah. Cleats and fracture distribution is observed in dark areas. The white bands are denser material as bedding planes.</p>
MPM-334-1: Fossil basicranium and endocranial volumes and CT-stack (Enantiornithes, Avialae)
<p>Among terrestrial vertebrates, only crown birds (Neornithes) rival mammals in terms of relative brain size and behavioural complexity. Relatedly, the anatomy of the avian central nervous system and associated sensory structures, such as the vestibular system of the inner ear, are highly modified with respect to those of other extant reptile lineages. However, a dearth of three-dimensional Mesozoic fossils has limited our knowledge of the origins of the distinctive endocranial structures of crown birds. Traits such as an expanded, flexed brain, a ventral connection between the brain and spinal column, and a modified vestibular system have been regarded as exclusive to Neornithes. Here, we demonstrate all of these 'advanced' traits in an undistorted braincase from an Upper Cretaceous enantiornithine bonebed in south-eastern Brazil. Our discovery suggests that these crown bird-like endocranial traits may have originated prior to the split between Enantiornithes and the more crownward portion of avian phylogeny over 140 million years ago, while coexisting with a remarkably plesiomorphic cranial base and posterior palate region. Altogether, our results support the interpretation that the distinctive endocranial morphologies of crown birds and their Mesozoic relatives are affected by complex trade-offs between spatial constraints during development.</p>
Investigation of the diagnostic importance and accuracy of CT in the chest compared to the RT-PCR test for suspected COVID-19 patients in Jordan
<p>As the world continues to battle the COVID-19 pandemic, Jordan is no exception. In order to improve the accuracy of diagnosis, researchers in Jordan have conducted an investigation into the diagnostic importance and accuracy of CT in the chest compared to the RT-PCR test for suspected COVID-19 patients.</p>
Micro-CT analysis of Katian radiolarians from the Malongulli Formation, New South Wales, Australia, and implications for skeletogenesis
<p><span>A diverse and well-preserved radiolarian assemblage from the Malongulli Formation, New South Wales, Australia contains 13 species representing ten genera and six families. One new genus: <em>Wiradjuri</em> n. gen. is introduced to accommodate pre-Devonian single-shelled entactiniid taxa and one new species: <em>Secuicollacta</em> <em>malongulliensis</em> n. sp. is recorded together with some previously described forms. The micro-structure of the 'rotasphaerid structure/primary unit' and the 'ectopic spicule' are investigated to validate their roles as fundamental units in the Secuicollactidae together with comprehensive documentation of the previously enigmatic <em>Pseudorotasphaera</em> internal skeleton.</span></p> <p><span>The results of this investigation suggest that, among all radiolarian genera that survived the </span>Late Ordovician Mass Extinction <span>event (LOME) and transitioned into the Silurian, <em>Secuicollacta</em>, <em>Haplotaeniatum</em>, and <em>Palaeoephippium</em> maintained stable body plans during the transition and were more successfully established. The selective advantages these lineages had during the LOME, were most likely spontaneous outcomes of the mode of structural development involving sequential skeletogenesis and a tendency to evolve towards simpler body plans. </span></p>
Cribra orbitalia in micro-CT
<p>The question answered by this project was how the morphological structure of a diploë changes according to the different degrees of CO expression. The basic technique was micro-CT scanning, which is one of the most accurate methods for analyzing the morphometry of anatomical objects, especially those of small dimensions.<br> A total of eleven superior surface eye orbits of children’s skeletons were used. On two of them, no changes typical for CO were observed. Four orbits had porosities less than 1 cm2 in area. On five superior surfaces of the orbits, porosities occupying an area greater than 1 cm2 were observed. The samples were scanned by a Bruker SkyScan 1172, and then the volumetric projections obtained in this way were reconstructed. In the next step, six parameters characterizing the structure of the spongy bone were measured, i.e., the number of trabeculae (Tb.N), the distance between the trabeculae (Tb.Sp), the thickness of the trabecular bone (Tb.Th), bone volume (BV/TV), bone surface area to volume ratio (BS/BV), and bone density (BS/TV).</p>
MICCAI FLARE22 Challenge Dataset (50 Labeled Abdomen CT Scans)
<p>This dataset was used as the labeled training set in MICCAI FLARE 2022 Challenge https://flare22.grand-challenge.org/.</p> <p>The CT images and pancreas annotations are from http://medicaldecathlon.com/</p> <p>The other organ annotations are from AbdomenCT-1K (research purpose only).</p> <p>If this dataset is useful in your research, please give credit to the following two papers:</p> <p>A large annotated medical image dataset for the development and evaluation of segmentation algorithms</p> <p>https://arxiv.org/abs/1902.09063</p> <p>AbdomenCT-1K: Is Abdominal Organ Segmentation a Solved Problem?</p> <p>https://ieeexplore.ieee.org/document/9497733</p>
Synchrotron CT image of hyaline cartilage lesion in the tibia of a 9 week old male STR/Ort mouse
<p>Figure from: Evans, L. A. E. (2023). <em>Imaging the articular osteochondral interface. </em>PhD Thesis. Royal Veterinary College, University of London, UK.</p> <p>Video of synchrotron CT slices showing hyaline cartilage lesion in the tibia of a 9 week old male STR/Ort mouse. Image obtained on the I13-2 beamline at Diamond Light Source, Oxfordshire, during beamtime MG24786-2. Scanning involved a bespoke cold stage designed by researchers including Dr Peter Rockett, Dr Saurabh Shah and Professor Peter Lee. Cold stage details can be found in a published research article with DOI: 10.1039/c7ra00642j. </p>
The gut microbiota in chronic obstructive pulmonary disease varies by CT-verified emphysema status
<p><strong><span>Background and aim</span> </strong></p> <p><span>The association of the gut microbiota to </span><span>chronic obstructive pulmonary disease (COPD)</span><span> phenotypes is underexplored. We aimed to compare</span><span> stool samples from COPD patients and healthy controls and relate findings to common COPD phenotypes. </span></p> <p><strong><span>Methods</span></strong></p> <p><span>Single-centre case-control study with 62 current and former smoking COPD patients and 49 controls. DNA was extracted from stool samples, and the V3V4-region of the bacterial 16S-rRNA gene was sequenced. Emphysema was defined based on thoracic computed tomography (CT thorax) low attenuating areas ≥/<10% at threshold -950 and -910 Hounsfield units respectively. Microbial data were analysed with QIIME 2 and R.</span></p> <p><strong><span>Results</span></strong></p> <p><span>The genus Veillonella was decreased and a genus belonging to class Clostridia was increased in COPD compared to healthy controls. Beta diversity measure Bray Curtis differed in emphysema compared to controls, and 27 genera were differentially abundant in emphysema vs. controls. Nine of these genera belonged to the family Lachnospiraceae. Lung function, blood counts and COPD assessment test scores were correlated with the relative abundance of several genera. Some of the genera showing the strongest correlation to lung function belonged to the family Lachnospiraceae. </span></p> <p><strong><span>Conclusion</span></strong></p> <p><span>We found small but statistically significant differences in the gut microbiota of COPD versus controls. Larger differences were seen in the gut microbiota according to CT-verified emphysema status. Correlations between the gut microbiota and lung function, blood cell counts, and CAT score were found. </span></p>
Learn2Reg Challenge: CT Lung Registration
<p>learn2reg_lungData_OriginalSize.zip contains the images used in the Learn2Reg challenge in the Lung CT task in the original resolution.</p> <p>For more information about this dataset go to: https://learn2reg.grand-challenge.org/</p> <p> </p>
A qualitative assessment of calcification across species and sexes of European Bufo toads using the micro-CT technique
<p><span>Micro-computed tomography </span><span>is a powerful tool towards the detailed reconstruction of internal and external morphology, in particular for ossified and other dense tissues. Here, we document and compare the amount of calcification in the skin of the head and the parotoids (the external skin glands) in males and females of the common and spined toads, <em>Bufo</em> <em>bufo</em> and <em>B. spinosus</em>. In some anurans including <em>Bufo</em> species, a specific acellular calcified tissue layer (the Eberth-Katschenko layer) within the dermis has been documented. Using micro-CT scan and standard histological techniques, we detected additional calcium deposits located in the dermal layer stratum spongiosum, above the Eberth-Katschenko layer. The data show that the level of calcification and the presence of the additional calcium deposits is size- and sex-related, increasing in the order from <em>B. bufo</em> males, <em>B. spinosus</em> males, <em>B. bufo</em> females to <em>B. spinosus</em> females. The least variable are <em>B. spinosus</em> females that have dense additional calcium deposits in parotoids, dorsal and ventral skin, as armour protecting their heads. Three-dimensional volume renderings and cross-sectional slices obtained by micro-CT scan used in this study indicate that this approach is a promising technique for further studies on <em>Bufo</em> skin anatomy and geographic variation in skin calcification.</span></p>
CT Data of Battery Pouch Cell with Defects
<p>These are CT slices as TIF files.</p> <p>Data: cubic voxels of (22 µm)³</p> <p>You may also open the included project file in VGStudio or the free myVGL viewer (https://www.volumegraphics.com/en/download-viewer.html) or other compatible software.</p> <p> </p> <p>The sample was prepared by Johannes Münch. For further details see the following paper:</p> <p><a href="https://doi.org/10.1002/ente.202300323">https://doi.org/10.1002/ente.202300323</a></p>
Non-Contrast CT Scans Dataset for Subarachnoid Hemorrhage: Bleeding Segmentation
<p>This dataset comprises non-contrast CT scans of patients admitted with subarachnoid hemorrhage. All scans are provided in the NIfTI format. Details of the image preprocessing, which encompasses anonymization, resampling, skull stripping, and intensity normalization, are available at <a href="https://github.com/smcch/Subarachnoid_Hemorrhage_segmentation_and_mortality_prediction">https://github.com/smcch/Subarachnoid_Hemorrhage_segmentation_and_mortality_prediction</a>.</p> <p>Each scan is accompanied by a corresponding NIfTI volume, showcasing the expert manual segmentation of the hemorrhage.</p>
CT reconstructions and 3D surface models of preserved impressions found on a Rijksmuseum terracotta sculpture
<p>This dataset contains 3D micro Computed Tomography (CT) reconstructions (*.tiff files) and 3D surface models (Wavefront OBJ files) of preserved impressions found on the terracotta sculpture "Study for a Hovering Putto", dated between 1735 and 1750, and attributed to Laurent Delvaux (Gent, 17 January 1696 – Nivelles, 24 February 1778, Rijksmuseum, BK-NM-9352). The preserved impressions are fingermarks and toolmarks, which we analyse in the manuscript "Artist profiling using micro-CT scanning of a Rijksmuseum terracotta sculpture" by Sero et al. (<a href="https://doi.org/10.1126/sciadv.adg6073">DOI: 10.1126/sciadv.adg6073</a>).</p> <p>Folder names correspond to the names assigned to each impression in the manuscript. Each folder contains a stack of *.tiff files and a "Segmentation.obj", which is the 3D model obtained from Otsu's segmentation method in Slicer3D. The stack of *tiff files and the 3D models can be visualized together in Slicer3D.</p>
Confocal and micro-CT data of Notocupes sp., BA202101
<p>This dataset contains the raw confocal laser scanning microscopy (CLSM) slices and X-ray microtomography (micro-CT) slices for the specimen of <em>Notocupes</em> sp. (BA202101) from mid-Cretaceous Burmese amber. This dataset is associated with the publication "New species of <em>Notocupes </em>from the Middle Jurassic Daohugou beds, with discussion on the circumscription of the genus" (DOI:10.11646/palaeoentomology.6.4.11).</p> <p>Confocal images were obtained with a Zeiss LSM710 confocal laser scanning microscope, using the 488 nm Argon laser excitation line. The original CZI files are provided, which could be opened by the ZEISS ZEN software.</p> <p>Micro-CT data were obtained with a Zeiss Xradia 520 Versa 3D X-ray microscope. Scanning parameters were as follows: isotropic voxel size, 14.096 μm; power, 3 W; acceleration voltage, 40 kV; exposure time, 4 s; projections, 2001. The TIFF stack is provided.</p>
Confocal and micro-CT data of Notocupes denticollis, holotype, STJ311
<p>This dataset contains the raw confocal laser scanning microscopy (CLSM) slices and X-ray microtomography (micro-CT) slices for the holotype of <em>Notocupes denticollis</em> (STJ311) from mid-Cretaceous Burmese amber. This dataset is associated with the publication "New species of <em>Notocupes </em>from the Middle Jurassic Daohugou beds, with discussion on the circumscription of the genus" (DOI:10.11646/palaeoentomology.6.4.11).</p> <p>Confocal images were obtained with a Zeiss LSM710 confocal laser scanning microscope, using the 488 nm Argon laser excitation line. The original CZI files are provided, which could be opened by the ZEISS ZEN software.</p> <p>Micro-CT data were obtained with a Zeiss Xradia 520 Versa 3D X-ray microscope. Scanning parameters were as follows: isotropic voxel size, 16.916 μm; power, 4 W; acceleration voltage, 50 kV; exposure time, 2 s; projections, 2001. The TIFF stack is provided.</p>
micro CT scan of Ice core, publication DOI:10.1109/TGRS.2023.3334867
<p>The dataset is used in the paper:</p> <p><strong>Bagherzadeh, Faramarz, et al. "Ice-Core Micro-CT Image Segmentation With Deep Learning and Gaussian Mixture Model." <em>IEEE Transactions on Geoscience and Remote Sensing</em> 61 (2023): 1-11.</strong><br><strong>DOI:10.1109/TGRS.2023.3334867</strong></p> <p><br>Polar ice cores 2D images of Micro CT scans that could be used for training and testing a deep neural network for image segmentation. This dataset is connected with the corresponding paper:<br>Title: "Ice Core micro-CT Image Segmentation with Deep Learning and Gaussian Mixture Model"</p> <p>There are mainly 3 specimens from Polar regions (snow, firn, and bubbly ice) with 60-micron resolution and a corresponding ground truth per input which was derived from a higher-resolution image with the methodology explained in the article.</p>
Dataset of 1000 CT Images of Thoracic Vertebrae with Segmentation
<p>Dataset of 1000 CT Images of Thoracic Vertebrae with Segmentation<br> </p> <p>B08 - DICOM scaled to 0-255</p> <p>B16 - DICOM 1:1 without Interslope</p> <p>B12 - DICOM scaled to 0-255 - division by 16 (4bits)</p> <p>BoneWnd - DICOM scaled to 0-255 - division by 8 (3bit), window of bone only</p>
Dataset of 1000 CT Images of Thoracic Vertebrae with Segmentation
<p>Dataset of 1000 CT Images of Thoracic Vertebrae with Segmentation</p> <p>B08 - DICOM scaled to 0-255</p> <p>B16 - DICOM 1:1 without Interslope</p> <p>B12 - DICOM scaled to 0-255 - division by 16 (4bits)</p> <p>BoneWnd - DICOM scaled to 0-255 - division by 8 (3bit), window of bone only<br> </p>
Automated segmentation of insect anatomy from micro-CT images using deep learning
<div>Three-dimensional (3D) imaging, such as micro-computed tomography (micro-CT), is increasingly being used by organismal biologists for precise and comprehensive anatomical characterization. However, the segmentation of anatomical structures remains a bottleneck in research, often requiring tedious manual work. Here, we propose a pipeline for the fully-automated segmentation of anatomical structures in micro-CT images utilizing state-of-the-art deep learning methods, selecting the ant brain as a test case. We implemented the U-Net architecture for 2D image segmentation for our convolutional neural network (CNN), combined with pixel-island detection. For training and validation of the network, we assembled a dataset of semi-manually segmented brain images of 76 ant species. The trained network predicted the brain area in ant images fast and accurately; its performance tested on validation sets showed good agreement between the prediction and the target, scoring 80% Intersection over Union (IoU) and 90% Dice Coefficient (F1) accuracy. While manual segmentation usually takes many hours for each brain, the trained network takes only a few minutes. Furthermore, our network is generalizable for segmenting the whole neural system in full-body scans, and works in tests on distantly related and morphologically divergent insects (e.g., fruit flies). The latter suggests that methods like the one presented here generally apply across diverse taxa. Our method makes the construction of segmented maps and the morphological quantification of different species more efficient and scalable to large datasets, a step toward a big data approach to organismal anatomy.</div>
Multimodal Fusion of Liquid Biopsy and CT Enhances Differential Diagnosis of Early-stage Lung Adenocarcinoma
<p>This research explores the potential of multimodal fusion for the differential diagnosis of early-stage lung adenocarcinoma (LUAD) (tumor sizes < 2 cm). It combines liquid biopsy biomarkers, specifically extracellular vesicle long RNA (evlRNA) and the computed tomography (CT) attributes.</p><p>It includes 4 files:</p><p>1. gene expression matrix : gene expression matrix for all samples (normalized read counts) .</p><p>2. evlRNA Rad features: 6 image features, 17 evlRNA features and labels</p><p>3. differentially expressed genes: Differentially expressed genes in LUAD patients compared with Benign individuals.</p><p>4. raw data: raw data used to for figure and table.</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.