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406 results for “micro-CT”
Dynamic 3D X-ray micro-CT data of a tablet dissolution in a water-based gel with dynamic changes in the scanning geometry
<p><strong>Summary</strong></p> <p>This submission contains a dynamic tomographic X-ray data of a tablet dissolving in a water-based gel. The data is collected over a 5-minute period during which the sample is rotated rapidly as effervescent bubbles are formed and travelling to the surface of the gel.</p> <p>This is the second experiment detailed in Case Study 3 in [Coban 2020], and this submission can be treated as a follow up to [Coban&Lucka 2019]. </p> <p> </p> <p><strong>Apparatus</strong></p> <p>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> </p> <p><strong>Sample Information</strong></p> <p>The setup consists of a store-bought denture cleaning tablet, placed at the bottom of a clear cylindrical plastic container. These tablets are typically designed to be fast-dissolving, and produce small and compact channels of bubbles. We use a denture cleaning tablet in particular as the dissolution time in water varies from 3 to 5 minutes, meaning the bubbles are produced at a slower rate. In addition, we use a store-bought water-based gel instead of water to slow down the bubble displacement during the experiment.</p> <p> </p> <p><strong>Experimental Plan</strong></p> <p>This experiment is performed such that 150 projections are collected over 360 degrees, for a total of 166 rotations, with exposure time 12 ms for each projection. This means that in total the submission contains 25000 projections. This experiment took 5 minutes of acquisition time, during which we (at user's command) zoom in onto the bottom of the sample holder (i.e. where the tablet rests). We later (again, at user's command) shift the view (i.e. the tube and the detector) upwards to the top of the sample to observe foaming on the surface. Finally, before the end of the 5-minute acquisition period, we zoom out to the original magnification. Every time the geometry undergoes a major change such as zooming in (which would affect the reconstruction), the system creates a new data settings file with the new geometrical information, appended by the projection number, therefore marking the change. However, since there is no major change created by the vertical shift of the tube and detector (as in no change in geometry that would affect the reconstructed images), there is no new data settings file for this event. </p> <p>The spatial resolution for this data is 193μm at the beginning (or end) of the experiment, which at an arbitrary point changes to 76μm. For a smooth data transfer, each projection image is binned down to the size of 486px-by-384px. No centrifugal force effect was observed on the bubbles travelling during the scan or in our test runs at the given rotational speed.</p> <p>All raw data (i.e. with no corrections) is made available in .tif format.</p> <p> </p> <p><strong>List of Contents</strong></p> <p>The contents of the submission is given below.</p> <ul> <li><strong>scan_1</strong>: A 5-minute dynamic CT data folder containing <ul> <li>dark-field (or closed-shutter) image, <em>di000000.tif,</em></li> <li>pre flat-field (or open-shutter before acquisition) image, <em>io000000.tif</em>,</li> <li>post flat-field (or open-shutter after acquisition) image, <em>io000001.tif</em>,</li> <li>raw (unprocessed or uncorrected) projections, <em>scan_*.tif</em> (25000 projections in total),</li> <li><em>data settings XRE.txt</em>, a text file with scanner metadata (this is the final geometry info file),</li> <li><em>data settings XRE_5220.txt</em> (geometry info recorded after the zoom-in)</li> <li><em>data settings XRE__22610.txt</em> (geometry info recorded after the zoom-out, same as <em>data settings XRE.txt</em>)</li> </ul> </li> </ul> <p> </p> <p><strong>Additional Links</strong></p> <p>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> </p> <p><strong>Contact Details</strong></p> <p>For more information or guidance in using these dataset, please get in touch with </p> <ul> <li>s.b.coban [at] cwi.nl</li> </ul> <p> </p> <p><strong>Acknowledgments</strong></p> <p>We thank Dr. Samuel McDonald and Prof. Philip Withers for the useful discussion, and Dr. Manuel Dierick for his advice in making this experiment possible.</p>
Dynamic 3D X-ray micro-CT data of a tablet dissolution in a water-based gel
<p><strong>Summary</strong></p> <p>This submission contains a dynamic tomographic X-ray data of a tablet dissolving in a water-based gel. The data is collected over a 5-minute period during which the sample is rotated rapidly as effervescent bubbles are formed and travelling to the surface of the gel.</p> <p>The data is made available as part of Case Study 3 in [Coban 2020].</p> <p> </p> <p><strong>Apparatus</strong></p> <p>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> </p> <p><strong>Sample Information</strong></p> <p>The setup consists of a store-bought denture cleaning tablet, placed at the bottom of a clear cylindrical plastic container. These tablets are typically designed to be fast-dissolving, and produce small and compact channels of bubbles. We use a denture cleaning tablet in particular as the dissolution time in water varies from 3 to 5 minutes, meaning the bubbles are produced at a slower rate. In addition, we use a store-bought water-based gel instead of water to slow down the bubble displacement during the experiment.</p> <p> </p> <p><strong>Experimental Plan</strong></p> <p> </p> <p>This experiment is performed such that 120 projections are collected over 360 degrees, for a total of 83 rotations, with exposure time 30 ms for each projection. This means that in total the submission contains 10000 projections. This took a total of 5 minutes of acquisition time, during which the tablet moved due to saturation but did not completely dissolve. The spatial resolution is 95μm, and the field of view was cropped to the boundaries of the sample holder (each projection image is of size 647px×768px). Our experimental setup allowed the collection of open and closed shutter (flat- and dark-field) images before decanting the gel onto the tablet. No centrifugal force effect was observed on the bubbles travelling during the scan or in our test runs at the given rotational speed.</p> <p>All raw data (i.e. no corrections) is made available in .tif format.</p> <p> </p> <p><strong>List of Contents</strong></p> <p>The contents of the submission is given below.</p> <ul> <li><strong>scan</strong>: A 5-minute dynamic CT data folder containing <ul> <li>dark-field (or closed-shutter) image, <em>di000000.tif,</em></li> <li>pre flat-field (or open-shutter before acquisition) image, <em>io000000.tif</em>,</li> <li>post flat-field (or open-shutter after acquisition) image, <em>io000001.tif</em>,</li> <li>raw (unprocessed or uncorrected) projections, <em>scan_*.tif</em> (10000 projections in total),</li> <li><em>data settings XRE.txt</em>, a text file with scanner metadata,</li> <li><em>script.txt</em> and <em>script_executed.txt</em> are the text files containing the list of commands the apparatus has executed.</li> </ul> </li> </ul> <p> </p> <p><strong>Additional Links</strong></p> <p>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> </p> <p><strong>Contact Details</strong></p> <p>For more information or guidance in using these dataset, please get in touch with </p> <ul> <li>s.b.coban [at] cwi.nl</li> </ul> <p> </p> <p><strong>Acknowledgments</strong></p> <p>We thank Dr. Samuel McDonald and Prof. Philip Withers for the useful discussion, and Dr. Manuel Dierick for his advice in making this experiment possible.</p> <p> </p>
ds-uct-003: Endodontic Instruments: X-Ray micro-CT of five endodontic files.
<p><strong>Summary</strong>:<br> .X-Ray micro-computed tomography (micro-CT) of five endodontic files used for the primary shaping of root canals, endodontic reintervention and supplementary cleaning methods.<br> .The 3D image was generated with an X-Ray micro-CT Scanner version Xradia Versa 510 from Zeiss performed by A Pereira at the UFF micro-CT Facility.<br> .For use of these data, please remember to cite the DOI of the Zenodo repository and relevant papers.</p> <p><strong>Details</strong>:<br> .flat-us (1024) - Voxel size: 10.0 μm; Sample-source: 30 mm; Sample-detector: 176 mm; Optical magnification: 0.4X; Filter: LE#1; Beam energy: 80 kV; Power: 7 W; Exposure time: 1.0 sec; Projections: 1600.<br> .xp-finish (1024) - Voxel size: 15.2 μm; Sample-source: 31 mm; Sample-detector: 110 mm; Optical magnification: 0.4X; Filter: LE#1; Beam energy: 80 kV; Power: 7 W; Exposure time: 0.4 sec; Projections: 1600.<br> .m2-30 (1024) - Voxel size: 18.2 μm; Sample-source: 39.5 mm; Sample-detector: 110 mm; Optical magnification: 0.4X; Filter: LE#1; Beam energy: 80 kV; Power: 7 W; Exposure time: 1.0 sec; Projections: 1600.<br> .m2r-25 (1024) - Voxel size: 18.2 μm; Sample-source: 39.5 mm; Sample-detector: 110 mm; Optical magnification: 0.4X; Filter: LE#1; Beam energy: 80 kV; Power: 7 W; Exposure time: 1.0 sec; Projections: 1600.<br> .reciproc-r25 (1024) - Voxel size: 18.2 μm; Sample-source: 39.5 mm; Sample-detector: 110 mm; Optical magnification: 0.4X; Filter: LE#1; Beam energy: 80 kV; Power: 7 W; Exposure time: 0.8 sec; Projections: 1600.</p> <p><strong>Contents</strong>:<br> ._info_ds-uct-003.txt<br> .ds-uct-003_endodontic_instruments_10um_8bits_flat-us.zip<br> .ds-uct-003_endodontic_instruments_15um_8bits_xp-finish.zip<br> .ds-uct-003_endodontic_instruments_18um_8bits_m2-30.zip<br> .ds-uct-003_endodontic_instruments_18um_8bits_m2r-25.zip<br> .ds-uct-003_endodontic_instruments_18um_8bits_reciproc-r25.zip</p>
ds-uct-006: Serjania Corrugata: X-Ray micro-CT of a Serjania corrugata (Sapindaceae) stem sample.
<p><strong>Summary</strong>:<br> .X-Ray micro-computed tomography (micro-CT) of a Serjania corrugata (Sapindaceae) stem sample, including both raw projection data and the final reconstructions, for a sigle resolution (voxel sizes of 40 μm).<br> .The 3D image was generated with an X-Ray micro-CT Scanner version Xradia Versa 510 from Zeiss performed by A Pereira at the UFF micro-CT Facility.<br> .For use of these data, please remember to cite the DOI of the Zenodo repository and relevant papers.</p> <p><strong>Details</strong>:<br> .Tomo - Voxel size: 40 μm; Sample-source: 120 mm; Sample-detector: 86.78 mm; Optical magnification: 0.4X; Filter: LE#1; Beam energy: 40 kV; Power: 3 W; Exposure time: 10.0 sec; Projections: 1600.</p> <p><strong>Contents</strong>:<br> ._info_ds-uct-006.txt<br> .ds-uct-006_serjania_corrugata_40um_8bits.zip<br> .ds-uct-006_serjania_corrugata_40um_1600p.txrm<br> .ds-uct-006_serjania_corrugata_40um_1600p_Drift.txrm<br> .ds-uct-006_serjania_corrugata_40um_1600p_recon.txm</p>
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
The genus Proceratium Roger, 1863 contains cryptic, subterranean ants that are seldom sampled and rare in natural history collections. Furthermore, most Proceratium specimens are extremely hairy and, due to their enlarged and curved gaster, often mounted suboptimally. As a consequence, the poorly observable physical characteristics of the material and its scarcity result in a rather challenging alpha taxonomy of this group. In this study, the taxonomy of the Chinese Proceratium fauna is reviewed and updated by combining examinations of traditional light microscopy with x-ray microtomography (micro-CT). Based on micro-CT scans of seven out of eight species, virtual 3D surface models were generated that permit in-depth comparative analyses of specimen morphology in order to overcome the difficulties to examine physical material of Proceratium. Eight Chinese species are recognized, of which three are newly described: Proceratium bruelheidei Staab, Xu & Hita Garcia, sp. n. and P. kepingmai sp. n. belong to the P. itoi clade and have been collected in the subtropical forests of southeast China, whereas P. shohei sp. n. belongs to the P. stictum clade and it is only known from a tropical forest of Yunnan Province. Proceratium nujiangense Xu, 2006 syn. n. is proposed as a junior synonym of P. zhaoi Xu, 2000. These taxonomic acts raise the number of known Chinese Proceratium species to eight. In order to integrate the new species into the existing taxonomic system and to facilitate identifications, an illustrated key to the worker caste of all Chinese species is provided, supplemented by species accounts with high-resolution montage images and still images of volume renderings of 3D models based on micro-CT. Moreover, cybertype datasets are provided for the new species, as well as digital datasets for the remaining species that include the raw micro-CT scan data, 3D surface models, 3D rotation videos, and all light photography and micro-CT still images. These datasets are available online (Dryad, Staab et al. 2018, http://dx.doi.org/10.5061/dryad.h6j0g4p).
FIGURE 12 in Taxonomy and nomenclature of some mainland SE-Asian Coeliccia species (Odonata, Platycnemididae) using micro-CT analysis
FIGURE 12. Virtual sections and volume rendering with micro-CT reconstruction of the genital ligula of Coeliccia scutellum (orientation bars: d dorsal, l lateral, p posterior, v ventral). A Virtual dorsal section from original image stack with genital ligula labeled in green, B Virtual sagittal section from original image stack with genital ligula labeled in green, C Transparent volume rendering of cuticle shows positioning of genital ligula within abdominal segment 2, ventral view, D Transparent volume rendering of cuticle shows positioning of genital ligula within abdominal segment 2, lateral view. Scale bars: 500Μm.
FIGURE 11 in Taxonomy and nomenclature of some mainland SE-Asian Coeliccia species (Odonata, Platycnemididae) using micro-CT analysis
FIGURE 11. Photos in life of Coeliccia pyriformis and Coeliccia cyanomelas. A Coeliccia pyriformis, male, Tam Đảo, northern Vietnam. B Coeliccia pyriformis, tandem, Tam Đảo, northern Vietnam. C Coeliccia pyriformis, male thorax and head dorsal, Tam Đảo, northern Vietnam. D Coeliccia cyanomelas, male head and thorax dorsolateral, Tam Đảo, northern Vietnam. E Coeliccia cyanomelas, male with four dorsal synthorax markings, Tam Đảo, northern Vietnam. F Coeliccia cyanomelas, male with two dorsal synthorax markings, Tam Đảo, northern Vietnam. All photos by Sebastién Delonglee.
FIGURE 10 in Taxonomy and nomenclature of some mainland SE-Asian Coeliccia species (Odonata, Platycnemididae) using micro-CT analysis
FIGURE 10. Coeliccia cyanomelas Tam Đảo, Vietnam. A head dorsal, B thorax dorsal, C thorax dorsolateral, D anal appendages dorsal, E anal appendages lateral, F anal appendages dorsolateral. Scale bars: 500Μm.
FIGURE 9. Coeliccia cyanomelas Taihanroku, Taiwan. A head dorsolateral, B in Taxonomy and nomenclature of some mainland SE-Asian Coeliccia species (Odonata, Platycnemididae) using micro-CT analysis
FIGURE 9. Coeliccia cyanomelas Taihanroku, Taiwan. A head dorsolateral, B prothorax and thorax dorsolateral, C prothorax and thorax dorsal, D anal appendages dorsal, E anal appendages lateral, F anal appendages dorsolateral, G left Fw, H left Hw. Scale bars: 500Μm.
FIGURE 8 in Taxonomy and nomenclature of some mainland SE-Asian Coeliccia species (Odonata, Platycnemididae) using micro-CT analysis
FIGURE 8. Genital ligulae as reconstructed from micro-CT (orientation bars: dl dorsolateral, l lateral, p posterior, v ventral, vl ventrolateral). A–B Genital ligula of C. pyriformis holotype, B–C genital ligula of C. cyanomelas.
FIGURE 7. Coeliccia pyriformis Holotype. A head dorsolateral, B in Taxonomy and nomenclature of some mainland SE-Asian Coeliccia species (Odonata, Platycnemididae) using micro-CT analysis
FIGURE 7. Coeliccia pyriformis Holotype. A head dorsolateral, B prothorax and thorax dorsolateral, C prothorax and thorax dorsal, D anal appendages dorsolateral, E anal appendages lateral, F anal appendages dorsal, G left Fw, H left Hw. Scale bars: 500Μm.
FIGURE 6 in Taxonomy and nomenclature of some mainland SE-Asian Coeliccia species (Odonata, Platycnemididae) using micro-CT analysis
FIGURE 6. Photos in life of Coeliccia hainanense and Coeliccia scutellum. A Coeliccia hainanense, male, Mount Wuzhishan, Hainan, China. Photo by Shanlian Mo). B Coeliccia hainanense, copula, Hui Shan, near Wanning, southeastern Hainan, China. Photo by Graham Reels. C Coeliccia hainanense, immature male, Nanlin Nature Reserve, near Wanning, southeastern Hainan, China. Photo by Graham Reels. D Coeliccia scutellum, female in tandem, Tam Đảo, northern Vietnam. Photo by Tom Kompier. E Coeliccia scutellum, male, Tam Đảo, northern Vietnam. Photo by Tom Kompier. F Coeliccia hainanense, male S7–10 and anal appendages, Mount Wuzhishan, Hainan, China. Photo by Schanlian Mo. G Coeliccia scutellum, male S7–10 and anal appendages, Tam Đảo, northern Vietnam. Photo by Tom Kompier. H Coeliccia scutellum, female in tandem, Tam Đảo, northern Vietnam. Photo by Sebastién Delonglee.
FIGURE 5 in Taxonomy and nomenclature of some mainland SE-Asian Coeliccia species (Odonata, Platycnemididae) using micro-CT analysis
FIGURE 5. Genital ligulae as reconstructed from micro-CT (orientation bars: dl dorsolateral, l lateral, p posterior, v ventral, vl ventrolateral). A–B Genital ligula of C. scutellum lectotype C–D genital ligula of C. scutellum from Tam Đảo, Vietnam E–F genital ligula of C. hainanense lectotype.
FIGURE 4. Coeliccia hainanense Lectotype. A head dorsolateral, B in Taxonomy and nomenclature of some mainland SE-Asian Coeliccia species (Odonata, Platycnemididae) using micro-CT analysis
FIGURE 4. Coeliccia hainanense Lectotype. A head dorsolateral, B prothorax and thorax dorsolateral, C anal appendages dorsal, D prothorax and thorax dorsal, E anal appendages dorsolateral, F appendages lateral, G left Fw, H left Hw. Scale bars: 500Μm.
FIGURE 1 in Taxonomy and nomenclature of some mainland SE-Asian Coeliccia species (Odonata, Platycnemididae) using micro-CT analysis
FIGURE 1. Mounting methods and detail of genital ligula. A Pinned specimen (Coeliccia scutellum) mounted for micro-CT scan, B papered specimen (Coeliccia scutellum) mounted for micro-CT scan, C macro-photograph (Zeiss MCr Camera) of C. scutellum genital ligula, showing thinness of flaps. Scale bar: 250Μm.
FIGURE 2. Coeliccia scutellum Lectotype. A head dorsolateral, B in Taxonomy and nomenclature of some mainland SE-Asian Coeliccia species (Odonata, Platycnemididae) using micro-CT analysis
FIGURE 2. Coeliccia scutellum Lectotype. A head dorsolateral, B prothorax and thorax dorsal, C prothorax and thorax lateral, D anal appendages lateral, E anal appendages dorsolateral, F anal appendages dorsal, G left Fw, H left Hw. Scale bars: 500Μm.
FIGURE 3 in Taxonomy and nomenclature of some mainland SE-Asian Coeliccia species (Odonata, Platycnemididae) using micro-CT analysis
FIGURE 3. Coeliccia scutellum Tam Đảo, Vietnam. A head dorsolateral, B thorax dorsal, C thorax lateral, D anal appendages dorsal, E anal appendages lateral, F anal appendages dorsolateral. Scale bars: 500Μm.
FIGURE 21 in 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
FIGURE 21. Comparison of (a) surface and (b) volume rendering of the same skeletal region of the same specimen; the acetabulum of Rhombophryne serratopalpebrosa (MNHN 1975.24). The surface rendering is that used in Scherz et al. (2014). The volume rendering was produced for this study. Note particularly the unossified state of the pubis in (b) compared to that reproduced in (a). The arrow indicates the end of the urostyle, which gradually thins towards its tip, but is shown to end abruptly in surface rendering due to the on/off characteristic of meshes.
FIGURE 17 in 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
FIGURE 17. Forelimb anatomy of the R. serratopalpebrosa species group showing (a) left manus in ventral view, (b) left radioulna in dorsal view, and left humerus in (c) lateral, (d) ventral, and (e) medial view. Abbreviations: cpl(s) = carpal(s), cr.lat = crista lateralis, cr.ven = crista ventralis, e.cap = eminentia capitata, ep.ul = epicondylus ulnaris.
FIGURE 16 in 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
FIGURE 16. The pectoral girdle of the R. serratopalpebrosa species group in ventral view, articulated (left) and laid flat (right). Abbreviations: scap.pa = scapula pars acromialis, scap.pg = scapula pars glenoidalis.
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