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102 results for “X–ray micro–CT”
Supplementary material 9 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) 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. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
3D PDF 9 : Explanation note: Zasphinctus wilsoni sp. n. holotype worker (MCZ-ENT-00512764). 3D PDF of volumetric surface rendering model of full body.
Supplementary material 14 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) 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. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
Video 1 : Explanation note: Zasphinctus obamai sp. n. paratype worker (CASENT0764127). 3D rotation video of volumetric surface rendering of head (most of antennae virtually removed).
Supplementary material 19 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) 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. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
Video 6 : Explanation note: Zasphinctus sarowiwai sp. n. holotype worker (CASENT0764654). 3D rotation video of volumetric surface rendering of metasoma (virtually separated from mesosoma and most of legs virtually removed).
Supplementary material 10 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) 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. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
3D PDF 10 : Explanation note: Zasphinctus wilsoni sp. n. holotype worker (MCZ-ENT-00512764). 3D PDF of volumetric surface rendering model of head (most of antennae virtually removed).
Supplementary material 15 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) 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. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
Video 2 : Explanation note: Zasphinctus obamai sp. n. paratype worker (CASENT0764127). 3D rotation video of volumetric surface rendering of mesosoma (head and metasoma mostly virtually removed).
Supplementary material 11 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) 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. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
3D PDF 11 : Explanation note: Zasphinctus wilsoni sp. n. holotype worker (MCZ-ENT-00512764). 3D PDF of volumetric surface rendering model of mesosoma (head and metasoma mostly virtually removed).
Supplementary material 12 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) 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. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
3D PDF 12 : Explanation note: Zasphinctus wilsoni sp. n. holotype worker (MCZ-ENT-00512764). 3D PDF of volumetric surface rendering model of metasoma (virtually separated from mesosoma and most of legs virtually removed).
Supplementary material 13 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) 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. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
3D PDF 13 : Explanation note: Zasphinctus sarowiwai sp. n. worker (CASENT0764652). 3D PDF of volumetric surface rendering of segmented mouthparts excluding mandibles (green= maxillae; yellow=labrum; orang=labium).
Romanesco X-ray micro-CT dataset
<p>X-ray micro-CT dataset of a romanesco cauliflower acquired on a Nikon XTH 225 at the 3D Imaging Center at the Technical University of Denmark (DTU). </p> <p><strong>romanesco.zip: </strong>The raw projection data as TIFF files along with geometric metadata.</p> <p><strong>romanesco_recon_2.zip:</strong> Reconstructed volume data using the Nikon software saved in binary format.</p> <p> </p> <p>Reconstruction can be carried out using for example the Core Imaging Library (CIL), <a href="https://ccpi.ac.uk/cil/">https://ccpi.ac.uk/cil/</a>, by loading in the data using the CIL NikonDataReader.</p>
Paired X-ray Micro CT Scanning and individual foraminifera isotopic analysis reveal (de)coupled changes in carbonate preservation and temperature
<p>To assess the coupling between drivers of isotopic variability and carbonate dissolution in foraminifera, we combine individual foraminiferal carbon and oxygen isotopic analyses (IFA) and X-ray MicroCT Scanning (XMCT)-based measurements of test densities (a proxy for the extent of post-depositional dissolution). As a proof-of-concept application of this approach, we analyze Globigerina bulloides tests from both coretop and downcore (latest Miocene/earliest Pliocene-aged) sediment from Ocean Drilling Project (ODP) Site 1088 (Agulhas Ridge).<br>Sediments from both the core intervals were wet-sieved over a 150 μm sieve and oven-dried at 55°C overnight. Individual tests of G. bulloides were picked from the >150 μm size fraction and gently brushed with the wet tip of a paintbrush to remove any adhering clay. Broken or partially fragmented tests were avoided. 25-50 individuals were mounted on a 1.2cm x 1 cm cardboard sample holder using double-sided carbon and imaged at a time on a Bruker Skyscan 1272 Micro-CT Scanner. In total, 123 individuals from the coretop sample and 88 individuals from the downcore sample were scanned.<br>Stable carbon (δ¹³C) and oxygen (δ¹⁸O) isotopic compositions of individual foraminifera were measured using a Kiel Carbonate Device IV coupled to a Thermo Fisher MAT 253 Plus Isotope Ratio Mass Spectrometer (IRMS). All individuals were weighed on a Sartorius ultramicrobalance before analysis, and only samples with mass >10 µg were analyzed as per the long-term precision setup of analyzing small quantities of carbonates on this machine. The XMCT-IFA dataset in this study consists of δ¹³C and δ¹⁸O values of 90 foraminifera (67 coretop and 23 downcore individuals). We compare population averages of XMCT parameters and isotopic compositions from both the coretop and downcore sediments.</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).
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
Open the record for dataset details and reuse information.
FIGURE 3. Pseudogarypus pangaea n in Description of a new fossil Pseudogarypus (Pseudoscorpiones: Pseudogarypidae) with the use of Xray microCT to penetrate opaque amber
FIGURE 3. Pseudogarypus pangaea n. sp., holotype, dorsal habitus reconstruction.
Supplementary material 23 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) 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. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
Video 10 : Data type: Video File (.mov)
Figure 1 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) 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. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
Figure 1 - Schematic line drawings illustrating the measurements used in this study. A Body in profile with measuring lines for PH, PTH, and WL B Mesosoma and metasoma in dorsal view with measuring lines for A3L, A3W, A4L, A4W, A5L, A5W, A6L, A6W, DML, PW, PTL, and PTW C Head in full-face view with measuring lines for HL, HW, and SL D Metafemur in dorsal view with measuring line for MFL.
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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)
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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.