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406 results for “micro-CT”
Fig. 6 in Non-destructive analysis of pathological belemnite rostra by micro-CT techniques
Fig. 6. Rostra of belemnite Gonioteuthis spp. A. RUB-Pal 11302, Campanian, Höver (NW-Germany) with forma aegra angulata (coll. U Frerichs). Surface images showing the knee-like morphology of the rostrum, and the attachment-base of an oyster, in lateral (A1, A4), dorsal (A2), and ventral (A4) views; note the weak furrows in A3. Median sections perpendicular to each other showing silicified areas (darker) and the broken phragmocone now filled with sediment, no additional internal feature visible (A5, A6). B. SNSB-BSPG-83246, Campanian, Höver (NW-Germany) with forma aegra angulata (coll. H. Keupp, leg. C. Spaeth). Surface images showing the knee-like morphology of the rostrum, in ventral (B1), lateral (B2, B4), and dorsal (B5) views. Cross section (B3). Median sections showing silicified areas specifically at places heavily bent (darker) (B6, B7); see also A5, A6 for the same phenomenon. Black box indicates close up in B7, showing the broken juvenile rostrum with growth increment (forma aegra clavata), and the phragmocone partially filled with pyrite (white).
Fig. 1 in Non-destructive analysis of pathological belemnite rostra by micro-CT techniques
Fig. 1. Rostrum of belemnite?Acrocoelites sp., PIMUZ 37346, Toarcian, Altdorf (SW-Germany) with forma aegra saepia (leg. M. Weissmüller). A. Overview A1, A2). B. Close-up of the two apices, showing the radial furrows covering the apex that represent the "normal" tip of the rostrum (B1–B5).
Micro-CT scans, whole-test meshes, and internal chamber segments of planktonic foraminifera for three-dimensional analysis of inter- and intra-specific variation in ontogenetic growth trajectories
<p> </p> <p>Here, we release tomographic reconstructions of 42 planktonic foraminifera from plankton tows and sediment traps, along with meshes and shrinkwrap meshes the whole tests and internal meshes of segmented chambers. Shrinkwrap meshes are test meshes that have been modified to close all pores and apertures in the test. Additionally, we have provided sample metadata for each specimen and volumetric measurements for the tests and chambers. This dataset was used in a study of ontogenetic growth in planktonic foraminifera and its variation within and among species.</p> <p> The CT-scans and reconstructions were obtained at Naturalis Biodiversity Center in Leiden, the Netherlands with a Zeiss Xradia 520 Versa micro-CT scanner. The meshes and segments were created at Yale University.</p> <ol> <li>Sample_Metadata.csv: Spreadsheet containing information on the sampling localities and dates for all specimens.</li> <li>Scan_data.csv: Spreadsheet containing metadata for all micro-CT scans including current strength, pixel size, voltage, image height, image width, and the number of images taken.</li> <li>Whole_Test_Measurements.csv: Spreadsheet containing measurements of linear dimensions (axis1, axis2, axis 3), total number of chambers, calcite test volume, calcite test surface area, shrinkwrap volumes, and and shrinkwrap surface areas for all specimens.</li> <li>Chamber_Measurements.csv: Spreadsheet containing measurements of individual internal chamber segments, including position from the final chamber (F-chamber), position from the first chamber (Chamber), volume, and surface area.</li> <li>CT_Scan_Stacks.zip: reconstructed micro-CT image stacks (.tif files) for each specimen.</li> <li>Meshes.zip: Meshes of the test calcite, the shrinkwrap, and the internal chamber segments for each specimen (.stl 3D mesh files). Regular test meshes are named with the format “SampleID.stl”, and shrinkwrap meshes are named “SampleID-WRAP.stl”. Chamber meshes are named “SampleID-CH#.stl” and “SampleID-CH#-Wrap.stl”. Chambers are numbered in relation to their position from the final chamber, with “CH1” being the final chamber and “CH2” being the penultimate chamber.</li> </ol> <p>This data is described and analyzed in the manuscript “Three-Dimensional Analysis of Inter- and Intraspecific Variation in Ontogenetic Growth Trajectories of Planktonic Foraminifera” submitted to the journal <em>Marine Micropaleontology.</em></p>
Linked collectors and determiners for: A review of the taxonomy and osteology of the Rhombophryne serratopalpebrosa species group (Anura: Microhylidae) from Madagascar, with comments on the value of volume rendering of micro-CT data to taxonomists.
Natural history specimen data linked to collectors and determiners held within, "A review of the taxonomy and osteology of the Rhombophryne serratopalpebrosa species group (Anura: Microhylidae) from Madagascar, with comments on the value of volume rendering of micro-CT data to taxonomists". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/c96e6bc4-729c-469c-9f1e-1f301d83357d">https://bionomia.net/dataset/c96e6bc4-729c-469c-9f1e-1f301d83357d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/c96e6bc4-729c-469c-9f1e-1f301d83357d">https://gbif.org/dataset/c96e6bc4-729c-469c-9f1e-1f301d83357d</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Endangered beauties: micro-CT cranial osteology, molecular genetics and external morphology reveal three new species of chameleons in the Calumma boettgeri complex (Squamata: Chamaeleonidae).
Natural history specimen data linked to collectors and determiners held within, "Endangered beauties: micro-CT cranial osteology, molecular genetics and external morphology reveal three new species of chameleons in the Calumma boettgeri complex (Squamata: Chamaeleonidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/99b3b009-f006-4146-b335-cbfdc2fcd60b">https://bionomia.net/dataset/99b3b009-f006-4146-b335-cbfdc2fcd60b</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/99b3b009-f006-4146-b335-cbfdc2fcd60b">https://gbif.org/dataset/99b3b009-f006-4146-b335-cbfdc2fcd60b</a>. Formatted as a Frictionless Data package.
Geometry models of specimens: Micro-CT, Mechanical, and Histological Examination of the Effect of Local Adjuvants on Porcine Cortical Bone Following Intralesional Curettage of Bone Tumors.
<p>Bone samples for micro CT measurements and reconstructed bone geometry from micro CT data.</p>
Platypsyllus castoris micro-CT datasets (head and thorax)
<p>Two micro-CT datasets of both head and thorax of the beaver beetle <em>Platypsyllus castoris</em> (Leiodidae, Coleoptera).</p> <p>The specimen was scanned at the MPI for the Science of Human History (Jena, Germany) with a SkyScan 2211 X-ray nanotomograph (Bruker, Knotich, Belgium), with an image spatial resolution of 0.30 μm (isotropic voxel size) using the following parameters: 60 kV, 250 μA, 4,300 ms exposure time, 0.20° rotation steps, frame averaging on (2), and using no filter. Projections were reconstructed by NRecon (Bruker, Knotich, Belgium) into TIFF files.</p>
Supplementary material S1. Donacia (Protodonacia) bienkowskii Bukejs and Alekseev subgen. et sp. nov., holotype, Nr. 3300.142 [RSKM], X-ray micro-CT volume rendering of the habitus without legs and antennae.
<p>Supplementary material S1 in paper: Bukejs A., Alekseev V.I. & McKellard R.C. First described reed beetle (Chrysomelidae: Donaciinae) from amber inclusion: member of the littoral community in the Eocene Baltic amber forest. Historical Biology.</p> <p> </p>
Supplementary material S3. Henoticus groehni sp. nov., holotype, No. 5087 [GPIH], X-ray micro-CT volume rendering of the left antenna.
<p>Supplementary material S3 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>
Morphology of Pulleniatina (planktonic foraminifera): Micro-CT internal volumes
Open the record for dataset details and reuse information.
Micro-CT data and associated MATLAB scripts from the skeleton of the sea urchin Cidaris rugosa at four different resolutions
Open the record for dataset details and reuse information.
Confocal and micro-CT data of Miniomma chenkuni, holotype, NIGP173375
<p>This dataset contains the raw confocal laser scanning microscopy (CLSM) slices and X-ray microtomography (micro-CT) slices for the holotype of <em>Miniomma chenkuni</em> (NIGP173375) from mid-Cretaceous Burmese amber. This dataset is associated with the publication "A miniaturized ommatid beetle in mid-Cretaceous Burmese amber (Coleoptera: Archostemata: Ommatidae)" (DOI:10.11606/1807-0205/2020.60.63).</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: isotropic voxel size, 2.1437 μm; power, 3 W; acceleration voltage, 40 kV; exposure time, 4 s; projections, 3001. The TIFF stack is provided.</p>
Treinamento Micro-CT
<p>Treinamento de Micro-CT (X-Ray Micro-Computed Tomography) realizado no micro-tomógrafo Xradia Versa 510 da Zeiss nas instalações da Universidade Federal Fluminense por André Pereira, no contexto de diversos projetos de pesquisa, financiados pela Shell e por diversos órgãos de fomento à pesquisa, em especial ao CNPq e a FAPERJ.</p>
Figure 21. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 21. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., paratype, 3D model, volume rendering, created with CTVox, virtual rotation and dissection. Movie available at: YouTube.
Figure 22. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 22. - Movie of Eupolybothrus cavernicolus Komerički & Stoev sp. n., holotype, filmed ex-situ in a plastic container. Movie available at: YouTube.
The role of injection method on residual trapping at the pore-scale in continuum-scale samples: raw micro-CT dataset
<p>The experiments in this work explore the role of a variable injection rate on gas saturation and residual trapping. There are 2 experiments in this work H2L (high to low injection rate) and L2H (low to high injection rate). The workflow for processing the micro-CT images to get the segmented images is described in [1]. </p><p>The following scans are included in this repository NB. all data for this repository is segmented micro-CT data.: </p><ol><li>Dry scan prior to experiment = <a href="https://zenodo.org/api/records/10145102/draft/files/05_dry_bin2_merged.tif/content">05_dry_bin2_merged.tif</a></li><li>Sample fully saturated with brine = <a href="https://zenodo.org/api/records/10145102/draft/files/07_wet_bin2_merged.tif/content">07_wet_bin2_merged.tif</a></li><li>H2L during high flow = <a href="https://zenodo.org/api/records/10145102/draft/files/09_h2lh_merged.tif/content">09_h2lh_merged.tif</a></li><li>H2L during low flow = <a href="https://zenodo.org/api/records/10145102/draft/files/11_h2ll_2_merged.tif/content">11_h2ll_2_merged.tif</a></li><li>H2L at the end of drainage (no flow) = <a href="https://zenodo.org/api/records/10145102/draft/files/16_dra1_pd5_merged.tif/content">16_dra1_pd5_merged.tif</a></li><li>H2L at the end of imbibition (no flow) = <a href="https://zenodo.org/api/records/10145102/draft/files/21_imb1_pi1_merged.tif/content">21_imb1_pi1_merged.tif</a></li><li>Sample fully resaturated with brine = <a href="https://zenodo.org/api/records/10145102/draft/files/28_wet2_bin2_merged.tif/content">28_wet2_bin2_merged.tif</a></li><li>L2H during low flow = <a href="https://zenodo.org/api/records/10145102/draft/files/29_2_l2hl_merged.tif/content">29_2_l2hl_merged.tif</a></li><li>L2H during high flow = <a href="https://zenodo.org/api/records/10145102/draft/files/30_l2hh_merged.tif/content">30_l2hh_merged.tif</a></li><li>L2H at the end of drainage (no flow) =<a href="https://zenodo.org/api/records/10145102/draft/files/31_dra2_pd1_merged.tif/content">31_dra2_pd1_merged.tif</a></li><li>L2H at the end of imbibition (no flow) =<a href="https://zenodo.org/api/records/10145102/draft/files/33_imb2_pi1_merged.tif/content">33_imb2_pi1_merged.tif</a></li></ol>
micro-CT dataset: Aphrodita longipalpa (Aphroditidae: Annelida) parasitized with Veneriserva pygoclava (Dorvilleidae: Annelida)
<p>This is the complete raw micro-CT dataset and the aligned image stacks generated with Nrecon (Bruker).</p> <p>It shows an adult sized <em>Aphrodita longipalpa</em> specimen, the host of a male and a female endoparasitic <em>Veneriserva pygoclava. </em>The specimen was formalin-fixed and ethanol-preserved and is deposited at the Benthic Invertebrate Collection of Scripps Institution of Oceanography (<a href="https://sioapps.ucsd.edu/collections/bi/catalog/A10919/?q=cf.+longipalpa&image=Any&idx=2">SIO-BIC A10919</a>). The specimen was stained with a contrast enriching phosphotungstic acid solution (0.3% PTA in 70% ethanol) for 3 weeks before scanning.<br> <br> A SkyScan 1272 µCT scanner (Bruker microCT, Kontich, Belgium) was used with the following parameters: 60 kV source voltage, 166 μA source current, 972 ms exposure and a camera resolution of 1224 × 820 px. The voxel resolution was 7.4 μm. </p>
Data file for Massé et al.'s article, "Unraveling the Life History of Past Populations through Hypercementosis: Insights into Cementum Apposition Patterns and Possible Etiologies using Micro-CT and Confocal Microscopy".
<p>This repository provides a supporting data file for the following research article:</p> <p>Massé L., d’Incau E., Souron A., Vanderesse N., Santos F., Maureille B., Le Cabec A. (2024) Unraveling the Life History of Past Populations through Hypercementosis: Insights into Cementum Apposition Patterns and Possible Etiologies Using Micro-CT and Confocal Microscopy. <em>Biology</em>, 13, 43. doi: <span><a href="https://doi.org/10.3390/biology13010043" target="_blank" rel="nofollow noopener noreferrer">10.3390/biology13010043</a></span></p> <p>For the detailed statistical analyses performed using this dataset, see Supporting Information 1 of the article.</p>
Bone point micro-CT raw data from Abric Romaní (Capellades, Barcelona, Spain)
<p>Raw data from micro-CT scanning of a bone point from Abric Romaní archaeological site (Capellades, Barcelona, Spain).</p>
Confocal and micro-CT data of Toxesbium kundratai, holotype, NIGP203543
<p>This dataset contains the raw confocal laser scanning microscopy (CLSM) slices and X-ray microtomography (micro-CT) slices for the holotype of <em>Toxesbium kundratai</em> (NIGP203543) from mid-Cretaceous Burmese amber. This dataset is associated with the publication "<em>Toxesbium</em> gen. nov., the first definitive member of Ernobiinae from mid-Cretaceous amber of northern Myanmar (Coleoptera: Ptinidae)" (DOI:10.1007/s12542-025-00715-2).</p> <p>Confocal images were obtained with a Zeiss LSM710 confocal laser scanning microscope, using the 488 nm (Argon) or 561 nm (DPSS 561-10) 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, 2.8752 μm; power, 3 W; acceleration voltage, 30 kV; exposure time, 2 s; projections, 3001. The TIFF stack is provided.</p>
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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
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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
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