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1,053 results for “Computed Tomography”
Computer-aided Veress needle guidance using endoscopic optical coherence tomography and convolutional neural networks
<p>During laparoscopic surgery, the Veress needle is commonly used in pneumoperitoneum establishment. Precise placement of the Veress needle is still a challenge for the surgeon. In this study, a computer-aided endoscopic optical coherence tomography (OCT) system was developed to effectively and safely guide Veress needle insertion. This endoscopic system was tested by imaging subcutaneous fat, muscle, abdominal space, and the small intestine from swine samples to simulate the surgical process, including the situation with small intestine injury. Each tissue layer was visualized in OCT images with unique features and subsequently used to develop a system for automatic localization of the Veress needle tip by identifying tissue layers (or spaces) and estimating the needle-to-tissue distance. We used convolutional neural networks (CNNs) in automatic tissue classification and distance estimation. The average testing accuracy in tissue classification was 98.53±0.39%, and the average testing relative error in distance estimation reached 4.42±0.56% (36.09±4.92 μm).</p> <p>The dataset is split into two parts:<br> (1) <strong>Classification</strong>. The zip file <em>veress_classification_raw_images.zip</em> contains 40K images from 8 swine samples where there are 1K images per layer (skin, fat, muscle, abdominal space, and small intestine)<br> (2) <strong>Regression</strong>. The zip file <em>veress_regression_raw_images.zip</em><strong> </strong>contains 8K images of the abdominal space from the same 8 swine samples, and the ground truth distance labels for each sample are found in the Excel files <em>S[1-8]_distance_measurement_20210803.xlsx.</em></p>
Dataset for quantifying avian inertial properties using calibrated computed tomography
<p>Estimating centre of mass and mass moments of inertia is an important aspect of many studies in biomechanics. Characterising these parameters accurately in three dimensions is challenging with traditional methods requiring dissection or suspension of cadavers. Here, we present a method to quantify the three-dimensional centre of mass and inertia tensor of birds of prey using calibrated computed-tomography (CT) scans. The technique was validated using several independent methods, providing body segment mass estimates within approximately 1% of physical dissection measurements and moment of inertia measurements with a 0.993 R<sup>2</sup> correlation with conventional trifilar pendulum measurements. Calibrated CT offers a relatively straightforward, non-destructive approach that yields highly detailed mass distribution data that can be used for three-dimensional dynamics modelling in biomechanics. Although demonstrated here with birds, this approach should work equally well with any animal or appendage capable of being CT scanned.</p>
Example data for "Calibration of X-ray computed tomography for surface topography measurement using metrological characteristics"
<p>Example raw data used to create figures during the conference paper "<a href="https://www.euspen.eu/knowledge-base/ICE21165.pdf"><em>Calibration of X-ray computed tomography for surface topography measurement using metrological characteristics</em></a>", presented at euspen’s 21st International Conference & Exhibition 2020</p> <p>Data in the ".datx" format are acquired using a ZYGO NexView NX2 coherence scanning interferometer.</p> <p>Data in the ".stl" format are acquired using a Nikon MCT 225 X-ray computed tomography instrument.</p>
Research compendium for 'Practical and technical aspects for the 3D scanning of lithic artefacts using micro-computed tomography techniques and laser light scanners for subsequent geometric morphometric analysis. Introducing the StyroStone protocol'
<p><strong>Abstract:</strong></p> <p>Here, we present a new method to scan a large number of lithic artefacts using three-dimensional (3D) scanning technology. Despite the rising use of high-resolution 3D surface scanners in archaeological sciences, no virtual studies have focused on the 3D digitization and analysis of small lithic implements such as bladelets, microblades, and microflakes. This is mostly due to difficulties in creating reliable 3D meshes of these artefacts resulting from several inherent features (i.e., size, translucency, and acute edge angles), which compromise the efficiency of structured light or laser scanners and photogrammetry. Our new protocol <em>StyroStone</em> addresses this problem by proposing a step-by-step procedure relying on the use of micro-computed tomographic technology, which is able to capture the 3D shape of small lithic implements in high detail. We tested a system that enables us to scan hundreds of artefacts together at once within a single scanning session lasting a few hours. As also bigger lithic artefacts (i.e., blades) are present in our sample, this protocol is complemented by a short guide on how to effectively scan such artefacts using a structured light scanner (Artec Space Spider). Furthermore, we estimate the accuracy of our scanning protocol using principal component analysis of 3D Procrustes shape coordinates on a sample of meshes of bladelets obtained with both micro-computed tomography and another scanning device (i.e., Artec Micro). A comprehensive review on the use of 3D geometric morphometrics in lithic analysis and other computer-based approaches is provided in the introductory chapter to show the advantages of improving 3D scanning protocols and increasing the digitization of our prehistoric human heritage.</p> <p><strong>Content List:</strong></p> <ul> <li><strong>S1. </strong>Step-by-step protocol entitled ‘StyroStone: A protocol for scanning and extracting three-dimensional meshes of stone artefacts using Micro-CT scanners’. Also available on protocols.io (dx.doi.org/10.17504/protocols.io.bzbfp2jn);</li> <li><strong>S2. </strong>Dataset with all raw semilandmark coordinate data (in .xlsx format) used in the validation study;</li> <li><strong>S3. </strong>AGMT3D project. The file “Validation Protocol-MorphoProject.mat” can be used to open the project in the software AGMT3D;</li> <li><strong>S4. </strong>Dataset in .csv format of the principal component score data of the validation study;</li> <li><strong>S5.</strong> R script used to create Figure 2 using the R package ggplot2;</li> <li><strong>S6. </strong>3D models of the experimental bladelets obtained with the Micro-CT scanner used in the validation study. Both .ply and .wrl formats are provided;</li> <li><strong>S7. </strong>3D models of the experimental bladelets obtained with the Artec Micro scanner used in the validation study. Both .ply and .wrl formats are provided.</li> </ul>
X-ray computed tomography aided engineering approach for non-crimp fabric reinforced composites [Data set]
<p>The finite element models behind the publication</p> <p>Auenhammer, R.M., Jeppesen, N., Mikkelsen, L.P., Dahl, V.A., Blinzler, B.J., Asp, L.E. Robust numerical analysis of fibrous composites from X-ray computed tomography image data enabling low resolutions, <em>Composites Science and Technology, </em><strong>224</strong>, 109458, <a href="https://doi.org/10.1016/j.compscitech.2022.109458">https://doi.org/10.1016/j.compscitech.2022.109458</a>, 2022. </p> <p>The x-ray scan data which the model is based on can be found in the following publication:</p> <p>Jeppesen, N., V.A. Dahl, A.N. Christensen, A.B. Dahl, L.P. Mikkelsen, Characterization of the fiber orientations in non-crimp glass fiber reinforced composites using structure tensor. IOP Conf. Ser.: Mater. Sci. Eng. 942, 012037, <a href="https://doi.org/10.1088/1757-899X/942/1/012037">https://doi.org/10.1088/1757-899X/942/1/012037</a> 2020</p> <p>and data-set</p> <p>Jeppesen N, Dahl V A, Christensen A N, Dahl A B and Mikkelsen L P 2020 Characterization of the fiber orientations in non-crimp glass fiber reinforced composites using structure tensor [data set] Zenodo. <a href="http://dx.doi.org/10.5281/zenodo.3877522">http://dx.doi.org/10.5281/zenodo.3877522.</a></p> <p> </p>
Characterizing Subjects Exposed to Humidifier Disinfectants Using Computed Tomography-based Latent Traits: A Deep Learning Approach
<p>Around nine million people had been exposed to toxic humidifier disinfectants (HDs) in Korea. HD-exposure may lead to HD-associated lung injuries (HDLI). However, many people who claimed HD exposure were not diagnosed of HDLI but still felt discomfort possibly due to the unknown effects of HD. Therefore, this study examined HD-exposed subjects with normal appearing lungs as well as unexposed subjects in clusters (subgroups) with distinct characteristics classified by deep-learning-derived computed-tomography (CT)-based tissue-pattern latent traits. Among the major clusters, cluster 0 (C0) and cluster 5 (C5) were dominated by HD-exposed and unexposed subjects, respectively. C0 was characterized by features attributable to lung inflammation or fibrosis compared with C5. The computational fluid and particle dynamics (CFPD) analysis suggested that the smaller airway sizes observed in the C0 subjects led to greater airway resistance and particle deposition in the airways. Accordingly, women appeared more vulnerable to HD-associated lung abnormality than men.</p>
Dataset for publication 'Automated computed tomography based parasitoid detection in mason bee rearings'
<p>Dataset corresponding to the publication <strong>Automated computed tomography based parasitoid detection in mason bee rearings </strong>published at PLOS One. This repository contains the training, validation and test data.</p>
Segmented primary phases of Al-alloy EN AW-2618A in the T61 state using synchrotron computed tomography
<p><span>This video shows the primary phases of the aluminum alloy EN AW-2618A in the T61 state measured by synchrotron computed tomography. </span></p> <p><span>Further information is provided in the file content.pdf. </span></p>
Cone beam computed tomography dataset of a knee phantom
<p>This is a cone beam computed tomography dataset of a custom-made knee phantom. The data was collected with Planmeca Viso G7 scanner. A total of 500 projections were collected. 100 kV with 80 mAs was used during the measurement. The data is stored in a mat-file that can be easily accessed in MATLAB, GNU Octave, Python, Julia, C/C++ and other languages. Only the flat field correction has been preapplied to the projection images, no other corrections have been done.</p> <p>Included are the FOV size, size of one detector pixel, the flat value, number of columns and rows in each projection image, the offset value for the object, the radians for the rotation of the panel (yaw/roll), the projection images themselves, the projection angles, the source to center of rotation and source to panel distances and the coordinates for the source and the center of the panel for each projection.</p> <p>The OMEGA software includes an example on how to use this dataset (all CBCT examples) in MATLAB/Octave and Python.</p>
Evaluation of orthodontically induced external root resorption following orthodontic treatment using Cone Beam Computed Tomography (CBCT): a systematic review and meta-analysis
<p>Datasets for all analyses performed in the paper.</p>
Ex-situ X-ray computed tomography data from two regions of non-crimp fabric based fibre composite under fatigue loading
<p>Ex-situ X-ray CT fatigue testing data published with data in brief: </p> <p>Jespersen, K. M., Glud, J. A., Zangenberg, J., Hosoi, A., Kawada, H., & Mikkelsen, L. P. (2018). <em>Ex-situ X-ray computed tomography, tension clamp and in-situ transilluminated white light imaging data of non-crimp fabric based fibre composite under fatigue loading. Data in Brief.</em></p> <p>as a part of the below journal paper.</p> <p>Jespersen, K. M., Glud, J. A., Zangenberg, J., Hosoi, A., Kawada, H., & Mikkelsen, L. P. (2018). Uncovering the fatigue damage initiation and progression in uni-directional non-crimp fabric reinforced polyester composite. Composites Part A.</p> <p>If using the data, please refer to one of the two.</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>
Ptychographic X-ray computed tomography data for three Portland cement pastes
<p>Mortars and concretes are ubiquitous materials with very complex hierarchical microstructures. To fully understand their main properties and to decrease their CO<sub>2</sub> footprints, a sound description of their (spatially-resolved) mineralogy is compulsory. Developing this knowledge is very challenging as about half of the volume of hydrated cement is a nanocrystalline component, calcium-silicate-hydrate (C-S-H gel). Furthermore, other poorly crystalline phases (e.g. iron-siliceous hydrogarnet or silica oxide) may coexist which are even more difficult to characterise. Traditional spatially-resolved techniques like electron microscopies involve complex sample preparation steps that often lead to artefacts (e.g. dehydration and microstructural changes). Here, we have used synchrotron ptychographic tomography for obtaining spatially-resolved information on three unaltered representative samples: neat Portland paste, Portland-calcite and Portland-fly ash blend pastes with spatial resolution below 100 nm in samples of up to 5×10<sup>4</sup> mm<sup>3</sup> of volume. For the neat Portland paste, the ptychotomographic study gave densities of 2.11 and 2.52 gcm<sup>-3</sup> and contents of 41.1 and 6.4 vol% for nanocrystalline C-S-H gel and poorly crystalline iron-siliceous hydrogarnet, respectively. Furthermore, the spatially-resolved volumetric mass density information has allowed to characterise inner product and outer product C-S-H gels. The average density of inner product C-S-H is smaller than that of outer product and its variability larger. Full characterisation of the pastes, including segmentation of the different components, is reported and the contents are compared with the results obtained by thermodynamical modelling.</p> <p> </p> <p> </p> <p> </p> <p>Ptychographic X-ray computed tomography provides 3D electron mass density and attenuation coefficient distributions of unaltered cement pastes with an isotropic resolution below 100 nm. This imaging technique allows quantitatively distinguishing between different components with very similar absorption contrast.</p> <p>Samples were measured at the cSAXS beamline: i) a neat Portland Cement (PC); ii) a PC-CC blend: 80 wt% of PC and 20 wt% of CaCO<sub>3</sub>, and iii) a PC-FA blend: 70 wt% of PC and 30 wt% of fly ash. The main aim of this study is to have a better insight of the microstructure of the amorphous/nanocrystalline gels with submicrometer spatial resolution. It is worth noting that it is possible to determine the gel mass density and water content within the attained 3D resolution (about 100 nm).</p> <p>Here, we focused on the spatial distribution of the different components and in the variation of the electron density values which are very related to the mass density values. Special attention is paid to the density values of the amorphous (or nanocrystalline) components. The electron and mass density values of the C-S-H gel for three pastes are thoroughly analyzed. The density values range from 2.05-2.10 g·cm<sup>-3</sup> for high density C-S-H gel for neat PC and PC-CC pastes to 1.80 g<sup>.</sup>cm<sup>-3</sup> for low density C-S-H gel in PC-FA paste. The density value of poorly crystalline iron-siliceous hydrogarnet component, r=2.52 g·cm<sup>-3</sup>, has also been determined.</p> <p>A summary of our ongoing research focused on the analyses of cement pastes by synchrotron PXCT is reported and discussed.</p> <p> </p> <p> </p> <p> </p> <p><strong>PC sample:</strong></p> <p>tomo_beta_S02536_to_S03341_Hann_freqscl_0.35_0xxx</p> <p>tomo_delta_S02536_to_S03341_Hann_freqscl_1.00_0xxx</p> <p> </p> <p><strong>PC-CC sample:</strong></p> <p>tomo_beta_S04692_to_S06001_Hann_freqscl_0.35_0xxx</p> <p>tomo_delta_S04692_to_S06001_Hann_freqscl_1.00_0xxx</p> <p> </p> <p><strong>PC-FA sample:</strong></p> <p>tomo_beta_S03351_to_S04661_Hann_freqscl_0.35_0xxx</p> <p>tomo_delta_S03351_to_S04661_Hann_freqscl_1.00_0xxx</p> <p> </p> <p> </p>
Fig. 7 in Micro-computed tomography for natural history specimens: a handbook of best practice protocols
Fig. 7. Setup of scanning containers. Images by HCMR micro-CT lab.
Fig. 2 in Micro-computed tomography for natural history specimens: a handbook of best practice protocols
Fig. 2. Schematic overview of the X-Ray generator.
X-ray computed tomography reveals that grain protrusion controls entrainment shear stress for entrainment of fluvial gravels: Dataset
<p>This is the dataset that accompanies a paper in Geology:</p> <p>Hodge RA, Voepel H, Leyland J, Sear DA, Ahmed S (2020). X-ray computed tomography reveals that grain protrusion controls entrainment shear stress for entrainment of fluvial gravels. Geology, 48(2), 149-153.</p> <p>The aim of this work was to understand how the properties of a sediment grain in a river bed affect the forces required to entrain that grain. This dataset presents the properties of 1055 sediment grains, which were meaured using CT scanning.</p>
Fig. 8 in A giant boring in a Silurian stromatoporoid analysed by computer tomography
Fig. 8. Idealised schematic drawing of Osprioneides kampto Beuck and Wisshak, igen. et isp. nov.
Processed model of a Computed Tomography scan of Roman window glass from Ephesos
<h1>Origin</h1> <p>The model is based on a tomography scan on an antique window glass fragment from Ephesos (today Efes, Turkey). The sample was contributed by the <em>Austrian Archaeological Institute</em>, Vienna, and has the inventory ID EVH12/1017/1322.</p> <p>The original scan data is published as</p> <p>Grobe and Schuetz (2021). Computed tomography scan of Roman window glass from Ephesos. <a href="https://doi.org/10.5281/zenodo.5651890">doi:10.5281/zenodo.5651890</a></p> <p>and is described in:</p> <p>Grobe, Noback, and Schuetz (2021). A model chain to simulate daylight in historic built environments. Presented at: <em>Widening Horizons - 27 Annual Meeting of the European Association of Archaeologists</em>, Kiel, Germany. <a href="https://doi.org/10.5281/zenodo.5495764">doi:10.5281/zenodo.5495764</a></p> <h1>Processing</h1> <p>The scan was processed to prepare its conversion into a simulation model, i.e.</p> <ul> <li>small isolated mesh components were deleted,</li> <li>disconnected and duplicate vertices and faces were removed,</li> <li>the outer surfaces were re-constructed by meshlab's implementation of the _Screened Poisson_ algorithm, and</li> <li>the resulting mesh was intersected with an exctruded rectangle.</li> </ul>
Computed tomography (CT) was used to study the interaction of NMs with the plant cell tissue in vivo using Zeiss Xradia 510 system on Arabidopsis thaliana leaf. T
<p>This work was supported by the National Research Facility for Lab X-ray CT (NXCT) at the µ-VIS X-ray Imaging Centre, University of Southampton, through EPSRC grant EP/T02593X.</p>
Fig. 2 in Redescription and phylogenetic position of the enigmatic Neotropical electric fish Iracema caiana Triques (Gymnotiformes: Rhamphichthyidae) using x-ray computed tomography
Fig. 2. Head of Iracema caiana, MZUSP 49205 (paratype), 345 mm SL.
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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)
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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.