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406 results for “micro-CT”
FIGURE 6. Cassidulus caribaearum Lamarck, 1801 in Synchrotron micro-CT scanning leads to the discovery of a new genus of morphologically conserved echinoid (Echinodermata: Cassiduloida)
FIGURE 6. Cassidulus caribaearum Lamarck, 1801 (CASIZ 222205 [neotype] [B–E, J–L]; CASIZ 112638 [A, F–I]), SEM images: valves of (A–B) triphyllous pedicellariae, (C–D) ophicephalous pedicellariae, (E–G) large tridentate pedicellariae ([H] detail of valve head), and (I–K) small tridentate pedicellariae ([L] detail of valve head). Scale bars: A–B, 15 µm; C–D, H, L, 30 µm; E–G, I–K, 100 µm.
Micro-CT scans of unloaded and loaded glenoid bone used for DVC
<p>Micro-CT (mCT) scans to estimate glenoid bone strain with Digital Volume Correlation (DVC). There are 8 mCT sets of the same sample. Sets mCT1 to mCT6 are unloaded glenoid for error estimation. Sets mCT7 and mCT8 are used for strain measurement: set mCT7 is unloaded and set mCT8 corresponds to 1500 N axial loading. Scans were performed consecutively pairwise: after each scan pair, the specimen was removed from the micro-CT and repositioned. Rigid registration of the fixed side and bone masking have been performed. Scans format is MHD.</p>
Data from: Revision of Icacinaceae from the Early Eocene London Clay flora based on X-ray micro-CT
The Early Eocene (Ypresian) London Clay Formation contains one of the most important fruit and seed assemblages from the Paleogene, including a large diversity of taxa (>350 spp.) preserved as pyrite permineralizations retaining 3D structure as well as anatomical detail. Despite the importance of the flora for understanding angiosperm biogeographic and evolutionary history, the majority of the fossil material has not been revisited since the original taxonomic treatments by E.M. Reid and M.E.J. Chandler. Given subsequent advances in our understanding of angiosperm phylogeny and fruit morphology, coupled with technological advances in imaging/visualizing fossil material, many of the taxa represented in the flora deserve further study. Here we present a revision of the pantropical family Icacinaceae using X-ray micro-computed tomography (micro-CT) images of 21 species from the flora. Based on the results, four new combinations are made, a new fossil-genus is established for a distinctive species with affinities to the Phytocreneae, and emended diagnoses are provided for eight taxa. Of the seven genera recognized from the flora, only one, Iodes Blume, is extant. This study offers important insights on the biogeographic and evolutionary history of Icacinaceae, which is one of the most abundant and diverse components of the flora from the London Clay Formation.
Data from: Next-generation morphological character discovery and evaluation: an X-ray micro-CT enhanced revision of the ant genus Zasphinctus Wheeler (Hymenoptera, Formicidae, Dorylinae) in the Afrotropics
New technologies for imaging and analysis of morphological characters offer opportunities to enhance revisionary taxonomy and better integrate it with the rest of biology. In this study, we revise the Afrotropical fauna of the ant genus Zasphinctus Wheeler, and use high-resolution X-ray microtomography (micro-CT) to analyse a number of morphological characters of taxonomic and biological interest. We recognise and describe three new species: Z. obamai sp. n., Z. sarowiwai sp. n., and Z. wilsoni sp. n. The species delimitations are based on the morphological examination of all physical specimens in combination with 3D scans and volume reconstructions. Based on this approach, we present a new taxonomic discrimination system for the regional fauna that consists of a combination of easily observable morphological characters visible at magnifications of around 80–100 ×, less observable characters that require higher magnifications, as well as characters made visible through virtual dissections that would otherwise require destructive treatment. Zasphinctus are rarely collected ants and the material available to us is comparatively scarce. Consequently, we explore the use of micro-CT as a non-invasive tool for the virtual examination, manipulation, and dissection of such rare material. Furthermore, we delineate the treated species by providing a diagnostic character matrix illustrated by numerous images and supplement that with additional evidence in the form of stacked montage images, 3D PDFs and 3D rotation videos of scans of major body parts and full body (in total we provide 16 stacked montage photographs, 116 images of 3D reconstructions, 15 3D rotation videos, and 13 3D PDFs). In addition to the comparative morphology analyses used for species delimitations, we also apply micro-CT data to examine certain traits, such as mouthparts, cuticle thickness, and thoracic and abdominal muscles in order to assess their taxonomic usefulness or gain insights into the natural history of the genus. The complete datasets comprising the raw micro-CT data, 3D PDFs, 3D rotation videos, still images of 3D models, and coloured montage photos have been made available online as cybertypes (Dryad, http://dx.doi.org/10.5061/dryad.4s3v1).
Micro-CT data from: Maternal care in mid-Cretaceous lagonomegopid spiders
<p>This dataset contains the raw Micro-CT data and a 3D CT reconstruction of a piece of Burmese amber CNU009432 from "Guo, X., Selden, P. and Ren, D. (2021) Maternal care in mid-Cretaceous lagonomegopid spiders. Proc. R. Soc. B.". These data shows the maternal care behaviour of an adult female lagonomegopid spider guarding her egg sac. </p> <p>Maternal care benefits the survival and fitness of offspring often at a cost to the mother's future reproduction and has evolved repeatedly throughout the animal kingdom. In extant spider species, this behaviour is very common and has different levels and diverse forms. However, evidence of maternal care in fossil spiders is quite rare. In this study,we describe four Mid-Cretaceous (approx. 99 Ma) amber specimens from northern Myanmar with an adult female, part of an egg sac and some spiderlings of the extinct family Lagonomegopidae preserved, which suggest that adult lagonomegopid females probably built and then guarded egg sacs in their retreats or nests, and the hatched spiderlings may have stayed together with their mother for some time. The newfossils represent early evidence of maternal care in fossil spiders, and enhance our understanding of the evolution of this behaviour.</p>
Supplementary material S1. Henoticus groehni sp. nov., holotype, No. 5087 [GPIH], X-ray micro-CT volume rendering of the habitus.
<p>Supplementary material S1 in paper: Bukejs A., Lyubarsky G.Yu., Alekseev V.I. The oldest fossil species of the genus <em>Henoticus</em> Thomson (Coleoptera: Cryptophagidae) from Eocene Baltic amber. <em>Historical Biology</em>.</p> <p> </p>
Supplementary material S2. Henoticus groehni sp. nov., holotype, No. 5087 [GPIH], X-ray micro-CT volume rendering of the habitus without legs.
<p>Supplementary material S2 in paper: Bukejs A., Lyubarsky G.Yu., Alekseev V.I. The oldest fossil species of the genus Henoticus Thomson (Coleoptera: Cryptophagidae) from Eocene Baltic amber. Historical Biology.</p> <p> </p>
SC4CT-2023: X-ray micro-CT datasets of Rubik's cube, Lego Gandalf, match head and frozen mouse.
<p>Four micro CT datasets acquired at the Technical University of Denmark in January 2023. Each dataset consists of zip-file containing both projection and vendor reconstruction data along with geometric metadata. </p> <p>The datasets were acquired by teachers and students of the DTU course Scientific Computing for Computed Tomography (SC4CT) in January 2023, <a href="https://people.compute.dtu.dk/pcha/HDtomo/SCforCT.html">https://people.compute.dtu.dk/pcha/HDtomo/SCforCT.html</a></p> <p> </p> <p><strong>Rubrics cube:</strong> Nikon micro-CT dataset of a Rubik's cube, showing the internal plastic and metal mechanisms.</p> <p><strong>Frosen mouse:</strong> Nikon micro-CT dataset of a frozen mouse. The sample slipped during the scan so contain a few movement artifacts which may be removed if using only short-scan data.</p> <p><strong>Match:</strong> Zeiss micro-CT dataset of a match head showing the constituents of the head.</p> <p><strong>Wizard:</strong> Zeiss micro-CT dataset of a Lego Gandalf mini figure with cape and staff.</p> <p> </p> <p>Reconstruction from the raw projection data can for example be done using the Core Imaging Library (CIL), <a href="https://ccpi.ac.uk/cil/">https://ccpi.ac.uk/cil/</a>, reading in the data using either the CIL ZeissDataReader or NikonDataReader.</p> <p> </p>
Data from: Next-generation morphological character discovery and evaluation: an X-ray micro-CT enhanced revision of the ant genus Zasphinctus Wheeler (Hymenoptera, Formicidae, Dorylinae) in the Afrotropics
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Data from: Revision of Icacinaceae from the Early Eocene London Clay flora based on X-ray micro-CT
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Micro-CT data from: Maternal care in mid-Cretaceous lagonomegopid spiders
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Data from: Systematics of the ant genus Proceratium Roger (Hymenoptera, Formicidae, Proceratiinae) in China – with descriptions of three new species based on micro-CT enhanced next-generation-morphology
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Data from: Whole-organism 3D quantitative characterization of zebrafish melanin by silver deposition micro-CT
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A five-tile tomographic micro-CT dataset of the oak sculpture "Holy woman with lantern" - part 2 of 2
<p><strong>Summary</strong><br> This submission contains a five-tile tomographic datasets of an oak sculpture <em>Holy woman with lantern, </em>belonging to the Rijksmuseum collection. The first part consists of the first three tiles, the second part of the last two tiles. The data is made available as part of [Bossema et al., 2020] and [Domínguez-Delmás et al., 2020]. </p> <p><strong>Apparatus</strong><br> The dataset is acquired using the custom-built and highly flexible CT scanner, FleX-ray Laboratory, developed by TESCAN-XRE, located at CWI in Amsterdam. This apparatus consists of a cone-beam microfocus X-ray point source that projects polychromatic X-rays onto a 1944-by-1536 pixels, 14-bit, flat detector panel. Full details can be found in [Coban 2020].</p> <p><strong>Sample Information</strong><br> The sample is an oak sculpture of a <em>Holy woman with lantern</em>, 35.8 cm high, c. 1500-1525 [Rijksmuseum inventory number BK-NM-9253, https://www.rijksmuseum.nl/en/collection/BK-NM-9253]. It was mounted on a wooden block on the rotation stage.</p> <p>See Figure 7 in [Bossema et al., 2020] for a picture of the object and the mount and [Domínguez-Delmás, 2020] for analysis of the reconstructed images. <em> </em><br> </p> <p><strong>Experimental Plan</strong><br> The data in this submission was collected to facilitate measurements of the tree rings (dendrochronological research) at different heights, and to illustrate the use of detector tiling for the investigation cultural heritage objects. To image the entire object, five vertical tiles were scanned at image resolution 67.8 micron. For each scan, the sample was rotated 360° in circular and continuous motion, with a dark-field (closed-shutter), and 2 flat-field (open-shutter) images taken before and after the acquisition. The datasets of Tile 1-4 consist of 2914 projections, the dataset of Tile 5 of 1500 projections.<br> All raw data (i.e. no corrections) is made available in .tif format.</p> <p><strong>List of Contents</strong><br> The content of the submission is given below.</p> <p>part 1:</p> <ul> <li><strong>t1: </strong>first vertical tile, bottom of sculpture</li> <li><strong>t2:</strong> second vertical tile</li> <li><strong>t3:</strong> third vertical tile</li> </ul> <p>part 2:</p> <ul> <li><strong>t4:</strong> fourth vertical tile</li> <li><strong>t5:</strong> fifth vertical tile, top of the sculpture</li> </ul> <p>Each data folder contains:</p> <ul> <li>dark-field (or closed-shutter) image, <em>di000000.tif</em>,</li> <li>flat-field (or open-shutter) image before acquisition, <em>io000000.tif</em>, and after acquisition, <em>io000001.tif</em>,</li> <li>raw (unprocessed or uncorrected) projections, <em>scan_*.tif</em>,</li> <li><em>data settings XRE.txt</em>, a text file with scanner metadata,</li> <li><em>scan settings.txt</em>, a text file with scanner metadata in more human readable format, and</li> <li><em>data settings XRE.ini</em>, a snapshot text file of basic geometry information at the start of a scan.</li> <li><em>script_executed.txt</em>, the text file containing the list of commands the apparatus has executed.</li> </ul> <p><strong>Additional Links</strong><br> These datasets are produced by the <a href="https://www.cwi.nl/research/groups/computational-imaging">Computational Imaging group</a> at Centrum Wiskunde & Informatica (CI-CWI). For any relevant Python/MATLAB scripts for the FleX-ray datasets, we refer the reader to our group's <a href="http://github.com/cicwi">GitHub page</a>.</p> <p><strong>Contact Details</strong><br> For more information or guidance in using these datasets, please get in touch with </p> <ul> <li>bossema [at] cwi.nl</li> </ul> <p><strong>Acknowledgments</strong><br> We thank Paul van Duin and Marta Domínguez Delmás for providing us with the opportunity to scan this interesting object.</p>
A five-tile tomographic micro-CT dataset of the oak sculpture "Holy woman with lantern" - part 1 of 2
<p><strong>Summary</strong><br> This submission contains a five-tile tomographic datasets of an oak sculpture <em>Holy woman with lantern, </em>belonging to the Rijksmuseum collection. The first part consists of the first three tiles, the second part of the last two tiles. The data is made available as part of [Bossema et al., 2020] and [Domínguez-Delmás et al., 2020]. </p> <p><strong>Apparatus</strong><br> The dataset is acquired using the custom-built and highly flexible CT scanner, FleX-ray Laboratory, developed by TESCAN-XRE, located at CWI in Amsterdam. This apparatus consists of a cone-beam microfocus X-ray point source that projects polychromatic X-rays onto a 1944-by-1536 pixels, 14-bit, flat detector panel. Full details can be found in [Coban 2020].</p> <p><strong>Sample Information</strong><br> The sample is an oak sculpture of a <em>Holy woman with lantern</em>, 35.8 cm high, c. 1500-1525 [Rijksmuseum inventory number BK-NM-9253, https://www.rijksmuseum.nl/en/collection/BK-NM-9253]. It was mounted on a wooden block on the rotation stage.</p> <p>See Figure 7 in [Bossema et al., 2020] for a picture of the object and the mount and [Domínguez-Delmás, 2020] for analysis of the reconstructed images. <em> </em><br> </p> <p><strong>Experimental Plan</strong><br> The data in this submission was collected to facilitate measurements of the tree rings (dendrochronological research) at different heights, and to illustrate the use of detector tiling for the investigation cultural heritage objects. To image the entire object, five vertical tiles were scanned at image resolution 67.8 micron. For each scan, the sample was rotated 360° in circular and continuous motion, with a dark-field (closed-shutter), and 2 flat-field (open-shutter) images taken before and after the acquisition. The datasets of Tile 1-4 consist of 2914 projections, the dataset of Tile 5 of 1500 projections.<br> All raw data (i.e. no corrections) is made available in .tif format.</p> <p><strong>List of Contents</strong><br> The content of the submission is given below.</p> <p>part 1:</p> <ul> <li><strong>t1: </strong>first vertical tile, bottom of sculpture</li> <li><strong>t2:</strong> second vertical tile</li> <li><strong>t3:</strong> third vertical tile</li> </ul> <p>part 2:</p> <ul> <li><strong>t4:</strong> fourth vertical tile</li> <li><strong>t5:</strong> fifth vertical tile, top of the sculpture</li> </ul> <p>Each data folder contains:</p> <ul> <li>dark-field (or closed-shutter) image, <em>di000000.tif</em>,</li> <li>flat-field (or open-shutter) image before acquisition, <em>io000000.tif</em>, and after acquisition, <em>io000001.tif</em>,</li> <li>raw (unprocessed or uncorrected) projections, <em>scan_*.tif</em>,</li> <li><em>data settings XRE.txt</em>, a text file with scanner metadata,</li> <li><em>scan settings.txt</em>, a text file with scanner metadata in more human readable format, and</li> <li><em>data settings XRE.ini</em>, a snapshot text file of basic geometry information at the start of a scan.</li> <li><em>script_executed.txt</em>, the text file containing the list of commands the apparatus has executed.</li> </ul> <p><strong>Additional Links</strong><br> These datasets are produced by the <a href="https://www.cwi.nl/research/groups/computational-imaging">Computational Imaging group</a> at Centrum Wiskunde & Informatica (CI-CWI). For any relevant Python/MATLAB scripts for the FleX-ray datasets, we refer the reader to our group's <a href="http://github.com/cicwi">GitHub page</a>.</p> <p><strong>Contact Details</strong><br> For more information or guidance in using these datasets, please get in touch with </p> <ul> <li>bossema [at] cwi.nl</li> </ul> <p> </p> <p><strong>Acknowledgments</strong><br> We thank Paul van Duin and Marta Domínguez Delmás for providing us with the opportunity to scan this interesting object.</p>
Data from: Beauty is more than skin deep: a non-invasive protocol for in vivo anatomical study using micro-CT
Microcomputed tomography (μCT) is a widely used tool in biomedical research, employed to investigate tissues and bone structures of small mammals in vivo. The application of in vivo μCT scanning in non-medical studies greatly lags behind the rapid advancements made in the biomedical field wherein the methodology has evolved to allow for longitudinal studies and eliminate the need to sacrifice the animal. Ecological and evolutionary studies often involve morphological measurements of a large sample of live animals; however, the potential of in vivo μCT imaging as a method for data acquisition has yet to be delineated. Here, we describe a protocol for in vivo μCT imaging of the internal anatomy of reptiles and amphibians, commonly used study organisms in ecological and evolutionary research. We consider the skeletal and extraskeletal (i.e. osteoderms) bones of a lizard as a case study to elucidate the potential of in vivo μCT imaging. First, we explore the effects of various parameter settings on radiation dose, scan time and image quality. Secondly, we develop a protocol to immobilize and restrain study organisms during scanning without need for the administration of anaesthetics and compare the results of the in vivo protocol to images obtained post-mortem. To immobilize animals, we replace the use of anaesthetics by cooling, thereby allowing the use of previously unsuitable rotating gantry μCT scanners that are readily available in scientific institutions. The resultant image quality of in vivo μCT scans is similar to that of post-mortem μCT scans, especially in the abdominal region. We discuss the effect of tube voltage, distance to X-ray source and metal filtration on radiation dose, and how these parameters could be altered to reduce the cumulative radiation dose while maintaining optimal image quality. The proposed in vivo μCT protocol offers a new approach to acquire anatomical information for non-biomedical studies. We offer specific suggestions as to how the protocol can be employed to suit a variety of model organisms.
FIGURE 4 in Automated segmentation of insect anatomy from micro-CT images using deep learning
FIGURE 4 Data augmentation. (a) Initial 2D image of a full head scan of an Atta texana ant specimen (original 1000 × 1000 px). Preprocessing is performed in two steps: (b) The image is cropped (original 520 × 520 px) around the brain area, keeping some of the muscles, nerves, and fibers that are close (or even attached) to the brain. The manual segmentation of the brain is indicated in blue. (c) Histogram equalization is used for additional augmentation, which enhances the contrast and projects the inner parts of the brain more clearly.
Micro-CT video files of melt embayments
<p>Videos of 3D volumes of olivine hosted melt embayments from the 2018 eruption at Mount Veniaminof. </p> <p>This work was performed at GeoSoilEnviroCARS (The University of Chicago, Sector 13), Advanced Photon Source (APS), Argonne National Laboratory. GeoSoilEnviroCARS was supported by the National Science Foundation – Earth Sciences (EAR – 1634415). Tomography capability developments were supported by DOE BES Geosciences (DE‐SC0020112). This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357.</p> <p> </p> <p>Segmenting was completed using<a href="https://www.slicer.org"> 3D Slicer. </a></p> <p>Segmentation colors are as follows:</p> <ul> <li>Brown: External silicate melt</li> <li>Green: Olivine host</li> <li>Black: Melt Embayments</li> <li>Lilac: Melt Inclusions</li> <li>Blue: Bubbles/Vesicles</li> <li>White: Oxides</li> </ul>
Confocal and micro-CT data of Isocryptophilus exilipunctus, holotype, NIGP203274
<p>This dataset contains the raw confocal laser scanning microscopy (CLSM) slices and X-ray microtomography (micro-CT) slices for the holotype of <em>Isocryptophilus exilipunctus</em> (NIGP203274) from mid-Cretaceous Burmese amber. This dataset is associated with the publication "An enigmatic Cretaceous beetle with possible affinity to Erotylidae (Coleoptera: Cucujiformia)" (DOI:10.1016/j.cris.2024.100075).</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, 3.3808 μm; power, 3 W; acceleration voltage, 40 kV; exposure time, 6 s; projections, 2801. The TIFF stack is provided.</p>
Confocal and micro-CT data of Trematosphindus newtoni, NIGP175114 (holotype) and NIGP175115 (paratype)
<p>This dataset contains the raw confocal laser scanning microscopy (CLSM) slices and X-ray microtomography (micro-CT) slices for the type specimens of <em>Trematosphindus newtoni</em> (holotype, NIGP175114, and paratype, NIGP175115) from mid-Cretaceous Burmese amber. This dataset is associated with the publication "New mid-Cretaceous cryptic slime mold beetles and the early evolution of Sphindidae (Coleoptera: Cucujoidea)" (DOI:10.3897/asp.79.e72724).</p> <p>Confocal images were obtained with a Zeiss LSM710 confocal laser scanning microscope, using 488 nm Argon laser excitation line. Both original CZI files and exported TIFF stacks are provided.</p> <p>Micro-CT data were obtained with a Zeiss Xradia 520 Versa 3D X-ray microscope. Scanning parameters were as follows: NIGP175114 [isotropic voxel size, 3.2569 μm; power, 4 W; acceleration voltage, 50 kV; exposure time, 1 s; projections, 2501]; NIGP175115 [isotropic voxel size, 2.3931 μm; power, 3 W; acceleration voltage, 40 kV; exposure time, 3 s; projections, 3001]. The TIFF stacks are provided.</p>
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Allen Brain Atlas
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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.