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204 results for “Microtomography”
FIGURE 1 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 1. Thin section and cathodoluminescence (CL) photomicrographs: Timaniella harkeri (GSC26406) (1-4), Spiriferina sp. (BS-1) (5-8), Stenoscisma timorense (BS-2) (9-12), Cleiothyridina baracoodensis (ML32) (13-16) and Tylothyris transversa (TeP) (17-20). 1-2, transmitted light (TL) (1) and corresponding CL images (2) of nonluminescent shell and infilling sediment composed of fine sand grains. 3-4, TL (3) and CL (4) images of nonluminescent associated with partially luminescent shell in the cardinal area of dorsal valve. 5-8, TL (5, 7) and CL (6, 8) images of nonluminescent associated with partially luminescent shell and luminescent infilling cement. 9-12, TL (9, 11) and CL (10, 12) images of luminescent shell with thin silicified layers and recrystallization along inner wall of brachiopod shell. 13, plane-polarized light (PPL) image of the original infilling sediment composed of calcareous sands. 14, PPL image showing the section of infilling cement. 15-16, TL (15) and CL (16) images of slightly luminescent shell. 17, PPL image of infilling comprising lime mud, calcite cement and relatively large, radially arranged, siliceous crystals. 18-19, TL (18) and CL (19) images of nonluminescent associated with partially luminescent shell. 20, CL image showing the section of nonluminescent internal shell structure (spiralia) preserved within infilling (This structure is hardly recognized in the TL image). Abbreviations: bs, brachiopod shell; im, infilling material; sl, silicified layer; cc, calcite crystal; NL, nonluminescent; SL, slightly luminescent; L, luminescent.
Linked collectors and determiners for: Revision of the Highly Specialized Ant Genus Discothyrea (Hymenoptera: Formicidae) in the Afrotropics with X-Ray Microtomography and 3 D Cybertaxonomy.
Natural history specimen data linked to collectors and determiners held within, "Revision of the Highly Specialized Ant Genus Discothyrea (Hymenoptera: Formicidae) in the Afrotropics with X-Ray Microtomography and 3 D Cybertaxonomy". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/56172c62-3e7c-4ab7-83d4-1dd9f5c57eb5">https://bionomia.net/dataset/56172c62-3e7c-4ab7-83d4-1dd9f5c57eb5</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/56172c62-3e7c-4ab7-83d4-1dd9f5c57eb5">https://gbif.org/dataset/56172c62-3e7c-4ab7-83d4-1dd9f5c57eb5</a>. Formatted as a Frictionless Data package.
Figure 13 in Phase contrast X-ray synchrotron microtomography and the oldest damselflies in amber (Odonata: Zygoptera: Hemiphlebiidae)
Figure 13. Electrohemiphlebia barucheli gen. et sp. nov., holotype ARC 372.1, apical part of hindwing.
Figure 20. Wing reconstructions. A–B in Phase contrast X-ray synchrotron microtomography and the oldest damselflies in amber (Odonata: Zygoptera: Hemiphlebiidae)
Figure 20. Wing reconstructions. A–B. Electrohemiphlebia barucheli gen. et sp. nov., holotype ARC 372.1. A, forewing. B, hindwing. C, Jordanhemiphlebia electronica Kaddumi gen. et sp. nov., holotype. Scale bars = 2 mm. N, nodus; Ax1, Ax2, primary antenodal crossveins; RA, radius anterior; RP, radius posterior; IR, intercalary radial veins; MA, median anterior; MP, median posterior; CuA, cubitus anterior; Pt, pterostigma.
Figure 11 in Phase contrast X-ray synchrotron microtomography and the oldest damselflies in amber (Odonata: Zygoptera: Hemiphlebiidae)
Figure 11. Electrohemiphlebia barucheli gen. et sp. nov., holotype ARC 372.1, nodal region of hindwing.
Figure 6 in Phase contrast X-ray synchrotron microtomography and the oldest damselflies in amber (Odonata: Zygoptera: Hemiphlebiidae)
Figure 6. Electrohemiphlebia barucheli gen. et sp. nov., holotype ARC 372.1, detail of fore legs white arrow for tibia).
Figure 1 in Phase contrast X-ray synchrotron microtomography and the oldest damselflies in amber (Odonata: Zygoptera: Hemiphlebiidae)
Figure 1. Electrohemiphlebia barucheli gen. et sp. nov., holotype ARC 372.1, habitus left lateral view.
Figure 3 in Phase contrast X-ray synchrotron microtomography and the oldest damselflies in amber (Odonata: Zygoptera: Hemiphlebiidae)
Figure 3. Electrohemiphlebia barucheli gen. nov., sp. nov., holotype ARC 372.1, habitus frontal view.
Figure 19 in Phase contrast X-ray synchrotron microtomography and the oldest damselflies in amber (Odonata: Zygoptera: Hemiphlebiidae)
Figure 19. Jordanhemiphlebia electronica Kaddumi gen. et sp. nov., holotype, basal half of wing. Scale bar = 1 mm.
Figure 2 in Phase contrast X-ray synchrotron microtomography and the oldest damselflies in amber (Odonata: Zygoptera: Hemiphlebiidae)
Figure 2. Electrohemiphlebia barucheli gen. et sp. nov., holotype ARC 372.1, habitus right lateral view.
"Raw data for the publication entitled -Phase and microstructure evolutions in LC3 binders by multi-technique approach including synchrotron microtomography-"
<p>"Raw data for the publication entitled -Phase and microstructure evolutions in LC3 binders by multi-technique approach including synchrotron microtomography-" this includes: raw data for calorimetry, MIP, LXRPD, NMR, PSD and thermal analysis.</p> <p> </p>
Data from: X-ray microtomography for ant taxonomy: an exploration and case study with two new Terataner (Hymenoptera, Formicidae, Myrmicinae) species from Madagascar
We explore the potential of x-ray micro computed tomography (μCT) for the field of ant taxonomy by using it to enhance the descriptions of two remarkable new species of the ant genus Terataner: T. balrog sp. n. and T. nymeria sp. n.. We provide an illustrated worker-based species identification key for all species found on Madagascar, as well as detailed taxonomic descriptions, which include diagnoses, discussions, measurements, natural history data, high-quality montage images and distribution maps for both new species. In addition to conventional morphological examination, we have used virtual reconstructions based on volumetric μCT scanning data for the species descriptions. We also include 3D PDFs, still images of virtual reconstructions, and 3D rotation videos for both holotype workers and one paratype queen. The complete μCT datasets have been made available online (Dryad, https://datadryad.org) and represent the first cybertypes in ants (and insects). We discuss the potential of μCT scanning and critically assess the usefulness of cybertypes for ant taxonomy.
Dataset for "Mix and measure - combining in situ X-ray powder diffraction and microtomography for accurate hydrating cement studies" paper
<p>Dataset for paper (doi: <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.cemconres.2023.107370" target="_blank" rel="noreferrer noopener">https://doi.org/10.1016/j.cemconres.2023.107370</a>) with the abstract: "It is reported an innovative methodology based on in situ MoKa1 laboratory X-ray powder diffraction (LXRPD) and microtomography (μCT) avoiding any sample conditioning. The pastes are injected in 2.0 mm capillaries and the extremes are just sealed. The measurements take place in the same region of the hydrating paste. Thick capillaries are key to avoiding self-desiccation, which dictates the need of high-energy X-ray radiation for the diffraction study. This approach has been tested with a PC 42.5 R paste having w/c=0.50. μCT data were collected at 12 hours and 1, 3, 7 and 79 days. LXRPD data were acquired at 1, 3, 7 and 77 days. In this proof-of-principle research, the same paste was also cured ex situ. Portlandite contents obtained by thermal analysis, ex situ powder diffraction, in situ mass balance calculation and in situ powder diffraction were 13.8, 13.1, 13.1 and 12.5 wt%, respectively. From the μCT study, the grey value histogram evolution with time showed a crossing point which allowed us to distinguish (appearing) hydrated products from (dissolving) unhydrated cement particles. Segmentations were carried out by global thresholding and the random forest approach (one type of supervised Machine Learning). The comparison of the segmented results for the unhydrated cement fraction and the Rietveld quantitative phase analysis outputs gave an agreement of 2%. The potential of this methodology to deal with more complex binders is also presented."</p>
Appendix 1. Revelieria groehni Sergi, Perkovsky et Reike, 2013, female, Baltic amber, JDC-9116 [JDC], X-ray microtomography volume rendering of the habitus.
<p>X-ray microtomography volume rendering of the habitus of Revelieria groehni Sergi, Perkovsky et Reike, 2013, female, Baltic amber, JDC-9116 [JDC].</p>
Appendix 2. Revelieria groehni Sergi, Perkovsky et Reike, 2013, female, Baltic amber, JDC-9116 [JDC], X-ray microtomography volume rendering of the forebody.
<p>X-ray microtomography volume rendering of the forebody of Revelieria groehni Sergi, Perkovsky et Reike, 2013, female, Baltic amber, JDC-9116 [JDC].</p> <p> </p>
Extended-field synchrotron microtomography for non-destructive analysis of incremental lines in human teeth cementum: example data
<h3>Abstract</h3> <p>Tooth cementum annulation (TCA) is used for determining age-at-death and stress periods based on yearly<br>deposited layers in the root cementum of human teeth. Traditionally, TCA analysis employs optical microscopy,<br>which requires cutting sections of the root and provides only sparse sampling in the third dimension. Ancient<br>teeth are often unique specimens that should not be damaged. In this imaging study, we show that extended-field<br>synchrotron radiation-based microtomography can be used to provide true micrometer resolution and full<br>coverage of the tooth for non-destructively surveying ancient teeth for incremental layers. To rapidly review the<br>root cementum layer of four teeth from an early 19th century cemetery with historical records of life events, we<br>developed a method for automatically enhancing incremental lines on virtual slices and for detecting regions with<br>strong incremental line appearances. Surveying large regions of the root cementum avoids missing high-contrast<br>incremental lines and hence improves TCA analysis as an alternative to irreversible slicing of the unique teeth.</p> <h3>Data</h3> <p>The repository contains the microtomography data from four teeth to enable reproducing Figures 6a,c,e,f in the associated publication, Tanner et al., "Extended-field synchrotron microtomography for non-destructive analysis of incremental lines in archeological human teeth cementum". Proceedings of SPIE 11840 (2021) 1184019. DOI: <a href="https://doi.org/10.1117/12.2595180" target="_blank" rel="noopener">10.1117/12.2595180</a>. Each dataset contains 57 tif slices around the selected slice selZ, i.e. selZ-28:selZ+28, as stated below.</p> <table> <tbody> <tr> <td><strong>Fig.</strong></td> <td><strong>Dataset</strong></td> <td><strong>Tooth</strong></td> <td><strong>selZ</strong></td> <td><strong>Slices</strong></td> <td><strong>sampleIdx</strong></td> <td><strong>hs</strong></td> <td><strong>Directory</strong></td> </tr> <tr> <td>6a</td> <td>tooth4_hs04_reco_selZ715.tar.gz</td> <td>T1</td> <td>715</td> <td>687:743</td> <td>2</td> <td>4</td> <td>dataDir1</td> </tr> <tr> <td>6c</td> <td>zahn_OKreC_probe1_hs02_reco_selZ1730.tar.gz</td> <td>T2</td> <td>1730</td> <td>1702:1758</td> <td>5</td> <td>2</td> <td>dataDir2</td> </tr> <tr> <td>6e</td> <td>zahn_probe1_hs04_reco_selZ275.tar.gz</td> <td>T3</td> <td>275</td> <td>247:303</td> <td>4</td> <td>4</td> <td>DataDir2</td> </tr> <tr> <td>6f</td> <td>zahn35_probe2_hs02_reco_selZ275.tar.gz</td> <td>T4</td> <td>275</td> <td>247:303</td> <td>3</td> <td>2</td> <td>dataDir1</td> </tr> </tbody> </table> <h3>Processing</h3> <p>Incremental teeth lines can be enhanced via the MATLAB programs available in the github repository <a href="https://github.com/unibas-bmc/enhanceIncrementalTeethLines">unibas-bmc/enhanceIncrementalTeethLines</a>.</p> <p>Please extract the data from <em>name</em>.tar.gz via unix command "tar -xzvf <em>name</em>.tar.gz" . Place the .tif files called reco_????.tif in directory "dataDir1" or "dataDir2" (see last column in table) using subdirectories based on the tooth name and heightstep, e.g. "tooth4_hs04/reco/" for dataset "tooth4_hs04_reco_selZ715.tar.gz". Then set the "sampleIdx" and "hs" parameter in "dataParameterDefinitionTeeth.m" as stated in the table above. Finally run "extractCementumPatchesEnhanceIL.m" to process the data.</p> <h3>Note</h3> <p>We are grateful for beamtime access at the Synchrotron SOLEIL, ANATOMIX beamline (experiment no. 20200712). ANATOMIX is an Equipment of Excellence (EQUIPEX) funded by the Investments for the Future program of the French National Research Agency (ANR), project NanoimagesX, grant no. ANR-11-EQPX-0031. </p> <p>We also thank the Citizen Science Project BBS “Bürgerforschungsprojekt Basel-Spitalfriedhof” for their time-consuming voluntary research regarding the historical sources of the samples.</p>
Cellular-resolution X-ray microtomography of an entire mouse brain: supporting data, scripts and parameters
<h2><strong>Abstract </strong></h2> <p><strong>Purpose:</strong> Histology is the gold standard for sub-cellular visualization of the mouse brain. It offers excellent in-plane resolution, but a comparably low out-of-plane resolution due to physical sectioning. X-ray microtomography does not require this trade-off. Tomographic imaging of the entire mouse brain with isotropic cellular resolution produces datasets of multiple terabytes in size. These data must be processed and made accessible to domain experts who may have only limited image processing knowledge.</p> <p><strong>Approach:</strong> Extended-field X-ray microtomography covering an entire mouse brain was performed. The 4,495 projections from 8 × 8 offset acquisitions were stitched to reconstruct a 15,000^3 voxel volume. The microtomography volume was non-rigidly registered to the Allen Mouse Brain Common Coordinate Framework v3 based on a combination of image intensity and landmark pairs.</p> <p><strong>Results: </strong>We present a 3.3 teravoxel dataset covering a full mouse brain with 0.65 μm voxel size. The data were block-wise transformed to a common coordinate system then stored in a public repository with a hierarchical format for navigation and overlay with anatomical annotations in online viewers such as Neuroglancer or siibra-explorer.</p> <p><strong>Conclusions:</strong> This study demonstrates X-ray imaging and data processing for a full mouse brain, augmenting current atlases by improving resolution in the third dimension by an order of magnitude. The data are publicly available and easily accessible for domain experts via browser-based viewers.</p> <h2>Data</h2> <p>File <code>b32_atlas_registration.zip</code> contains the input data, parameter files and output data of affine and non-rigid registration of the 32 x 32 x 32 voxels downsampled microtomography image to the Allen Mouse Brain Common Coordinate Framework v3.</p> <p>File <code>create_sharded_Neuroglacer_format.pdf</code> will provide instructions how to create gZip-compressed, sharded, pre-computed Neuroglancer format via the open source software <a href="https://github.com/seung-lab/igneous">igneous</a>. This is currently still missing.</p> <h2>Processing</h2> <p>Reconstruction of extended field microtomography images mit projection stitching in horizontal and vertical direction was achieved with our software pipeline <a href="https://github.com/unibas-bmc/mosaicreconstruction">mosaicreconstruction</a>.</p> <p>The 32 x 32 x 32 voxels downsampled microtomography image was registered with the open source software <a href="https://elastix.lumc.nl/">elastix (and transformix)</a>. The <code>elastix.log</code> file states the used command line options. Directory names require adapting for reproducing the results. </p> <p>As terabyte large images and the non-rigid transformation parmeters do not fit into memory, we developed a distributed hierarchical approach with sub-volume transformations for the high resolution level, see <a href="https://github.com/unibas-bmc/LargeVolumeTransformix">LargeVolumeTransformix</a>. The high resolution tomography volume (moving volume) was warped to the atlas (fixed volume) by dividing the fixed space into 12 × 12 × 12 target subregions, such that the axes-aligned extended moving image subregion, the moving image transformed subregion, and the transformation parameters all fit in memory for an isotropic target voxel resolution of 0.65 μm.</p>
Cupes groehni Kirejtshuk, 2005, Rovno amber, JDC 8373 [JDC], X-ray microtomography volume rendering of the habitus.
<p><em>Cupes groehni</em> Kirejtshuk, 2005, Rovno amber, JDC 8373 [JDC], X-ray microtomography volume rendering of the habitus.</p>
Data from: Revision of the highly-specialized ant genus Discothyrea (Hymenoptera: Formicidae) in the Afrotropics with x-ray microtomography and 3D cybertaxonomy
Discothyrea Roger, 1863 is a small genus of proceratiine ants with remarkable morphology and biology. However, due to cryptic lifestyle Discothyrea are poorly represented in museum collections and their taxonomy has been severely neglected. We perform the first comprehensive revision of Discothyrea in the Afrotropical region through a combination of traditional and 3D cybertaxonomy based on micro-CT. Species diagnostics and morphological character evaluations are based on examinations of all physical specimens and virtual analyses of 3D surface models generated from micro-CT data. Additionally, we applied virtual dissections for detailed examinations of cephalic structures to establish terminology based on homology for the first time in Discothyrea. The complete datasets comprising micro-CT data, 3D surface models and videos, still images of volume renderings, and coloured stacked images are available online as cybertype datasets (Hita Garcia et al., dryadXXXXXXXXXX). We define two species complexes (D. oculata and D. traegaordhi complexes) and revise the taxonomy of all species through detailed illustrated diagnostic character plates, a newly developed identification key, species descriptions, and distribution maps. In total, we recognize 20 species, of which 15 are described as new. We also propose D. hewitti Arnold, 1916 as junior synonym of D. traegaordhi Santschi, 1914 and D. sculptior Santschi, 1913 as junior synonym of D. oculata Emery, 1901. Also, we designate a neotype for D. traegaordhi to stabilize its status and identity, and we designate a lectotype for D. oculata. The observed diversity and endemism are discussed within the context of Afrotropical biogeography and the oophagous lifestyle. ESA Editorial Office: 3 Park Place, Suite 307, Annapolis, MD 21401-3722, USA. Editorial Office Phone: 1-301-731-4535.
Figure 16. Hemiphlebia mirabilis Selys, 1869 in Phase contrast X-ray synchrotron microtomography and the oldest damselflies in amber (Odonata: Zygoptera: Hemiphlebiidae)
Figure 16. Hemiphlebia mirabilis Selys, 1869, anterior view of head.
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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)
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.