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102 results for “X–ray micro–CT”
Fig. 5. 3D in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 5. 3D visualizations of Micro-CT data of the deformed shell, (MCSMNH-PMSL-Moll.-FVelkovrh 34099[spm4]) from Cetinska pećina. A. Aperture view. B. Aperture facing right view. C. Apical view. D. Dorsal view. E. Aperture facing left view. F. Ventral view with umbilicus covered by last quarter of shell whorl.
Fig. 1 in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 1. Map showing Western Balkan cave localities of populations of Zospeum Bourguignat, 1856. Cave localities are indicated in red.
Fig. 3 in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 3. Light microscopic images of shells from the caves Benetina pećina (SE Bosnia and Herzegovina) and Cetinska pećina (Montenegro) with specimen labels. A. Zospeum troglobalcanicum Absolon, 1916, lectotype (NHMW Moll.Coll.Edlauer 32.749) from Benetina pećina. B–C. Zospeum tortuosum Jochum & Ruthensteiner sp. nov., paratypes (MCSMNH-PMSL-Moll.-FVelkovrh 34099[spm2-3]) from Cetinska pećina. D. Zospeum tortuosum Jochum & Ruthensteiner sp. nov., holotype (MCSMNHPMSL-Moll.-FVelkovrh 34099[spm1]) from Cetinska pećina. E. Deformed shell (MCSMNH-PMSLMoll.-FVelkovrh 34099[spm4]) from Cetinska pećina.
Fig. 14. 3D in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 14. 3D visualizations of Micro-CT data of Zospeum constrictum Jochum & Ruthensteiner sp. nov. (NHMW Mol.Coll.Edlauer 16.693). A–F. Holotype. A. Aperture and dorsal views. B. Aperture facing right view. C. Apical view showing upper right side of final whorl tucked underneath spire. D. Dorsal view. E. Aperture facing left view. F. Ventral view. G–L. Paratype (Fig. 13B). G. Aperture view. H. Aperture facing right view. I. Apical view showing upper right side of final whorl tucked underneath spire. J. Dorsal view. K. Aperture facing left view. L. Ventral view.
Fig. 20. 3D in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 20. 3D visualizations of Micro-CT data of Zospeum sp. 2, Taleža pećina, bei Trebinje, BiH, presented as Z. troglobalcanicum in Inäbnit et al. 2021 (NMBE 553414/1 (ex RSC 1981). A. Aperture view showing low, ridge-like fold on inner penultimate whorl. B. Aperture facing right view showing smooth columella. C. Apical view. D. Dorsal view. E. Aperture facing right view. F. Ventral view showing peristome edge directly parallel to umbilical depression.
Fig. 8. 3D in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 8. 3D visualizations of Micro-CT data of shells from the caves Lipska pećina and Duboki do (Montenegro). A–F. Zospeum troglobalcanicum Absolon, 1916 (MCSMNH-PMSL-Moll.-FVelkovrh 29603) (Fig. 7A). A. Aperture view. B. Aperture facing right view. C. Apical view. D. Dorsal view. E. Aperture facing left view. F. Ventral view showing reduced umbilical depression. G–L. Zospeum dubokidoense Jochum & Ruthensteiner sp. nov., holotype (MCSMNH-PMSL-Moll.-FVelkovrh 30360[spm1]). G. Aperture view. H. Aperture facing right view. I. Apical view. J. Dorsal view. K. Aperture facing left view. L. Ventral view showing no umbilical depression.
Supplementary material S2. Leiestes tomaszewskae sp. nov., holotype, Nr. 6723 [MAIG], X-ray micro-CT volume rendering of the habitus (without legs).
<p>X-ray micro-CT volume rendering of the habitus (without legs) of <em>Leiestes</em> <em>tomaszewskae</em> sp. nov., holotype, Nr. 6723 [MAIG].</p>
Supplementary material S1. Leiestes tomaszewskae sp. nov., holotype, Nr. 6723 [MAIG], X-ray micro-CT volume rendering of the habitus.
<p>X-ray micro-CT volume rendering of the habitus of <em>Leiestes</em> <em>tomaszewskae</em> sp. nov., holotype, Nr. 6723 [MAIG].</p>
Supplementary material S3. Leiestes tomaszewskae sp. nov., holotype, Nr. 6723 [MAIG], X-ray micro-CT volume rendering of the right antenna.
<p>X-ray micro-CT volume rendering of the right antenna of <em>Leiestes</em> <em>tomaszewskae</em> sp. nov., holotype, Nr. 6723 [MAIG].</p>
Supplementary material S1. Ptilodactyla eocenica Kundrata, Bukejs and Blank, 2021, male, SIZK ZH-85, X-ray micro-CT volume rendering of the habitus.
<p>Supplementary material S1 in paper: Telnov D., Perkovsky E.E., Kundrata R., Karišs K., Vasilenko D.V., Bukejs A. Revealing Palaeogene distribution of the Ptilodactylidae (Insecta: Coleoptera): the first <em>Ptilodactyla</em> Illiger, 1807 records from Rovno amber of Ukraine. <em>Historical Biology</em>.</p>
Supplementary material S2. Ptilodactyla eocenica Kundrata, Bukejs and Blank, 2021, male, SIZK ZH-85, X-ray micro-CT volume rendering of the forelegs.
<p>Supplementary material S2 in paper: Telnov D., Perkovsky E.E., Kundrata R., Kairišs K., Vasilenko D.V., Bukejs A. Revealing Palaeogene distribution of the Ptilodactylidae (Insecta: Coleoptera): the first <em>Ptilodactyla</em> Illiger, 1807 records from Rovno amber of Ukraine. <em>Historical Biology</em>.</p>
Supplementary material S3. Ptilodactyla eocenica Kundrata, Bukejs and Blank, 2021, male, SIZK ZH-85, X-ray micro-CT volume rendering of the hind legs.
<p>Supplementary material S3 in paper: Telnov D., Perkovsky E.E., Kundrata R., Kairišs K., Vasilenko D.V., Bukejs A. Revealing Palaeogene distribution of the Ptilodactylidae (Insecta: Coleoptera): the first <em>Ptilodactyla</em> Illiger, 1807 records from Rovno amber of Ukraine. <em>Historical Biology</em>.</p>
Supplementary material S5. Ptilodactyla odnosum Telnov, Perkovsky, Kundrata and Bukejs sp. nov., holotype, MAIG-6710, female, X-ray micro-CT volume rendering of the left antenna.
<p>Supplementary material S5 in paper: Telnov D., Perkovsky E.E., Kundrata R., Kairišs K., Vasilenko D.V., Bukejs A. Revealing Palaeogene distribution of the Ptilodactylidae (Insecta: Coleoptera): the first <em>Ptilodactyla </em>Illiger, 1807 records from Rovno amber of Ukraine. <em>Historical Biology</em>.</p>
Supplementary material S4. Ptilodactyla odnosum Telnov, Perkovsky, Kundrata and Bukejs sp. nov., holotype, MAIG-6710, female, X-ray micro-CT volume rendering of the habitus.
<p>Supplementary material S4 in paper: Telnov D., Perkovsky E.E., Kundrata R., Kairišs K., Vasilenko D.V., Bukejs A. Revealing Palaeogene distribution of the Ptilodactylidae (Insecta: Coleoptera): the first <em>Ptilodactyla</em> Illiger, 1807 records from Rovno amber of Ukraine. <em>Historical Biology</em>.</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>
Manual 4D annotations of Micro X-ray CT time-series (4D dataset)
<p>The 4D (3D+time) manual annotations of https://doi.org/10.5281/zenodo.4293394. For the annotation the SuRVoS workbench was used (https://doi.org/10.5281/10.5281/zenodo.247547) and our proposed hidden Markov model (HMM-T, https://doi.org/10.5281/zenodo.4416013 ) designed to refine 4D semantic segmentations made by a 3D semantic segmentation CNN after its applied on 4D data. Only slices 740-742 and 747-749 (refining to the first axis) are partially annotated. We acknowledge Diamond Light Source for the time on I13-2 under proposal mt9396.</p>
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>
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