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160 results for “X-ray CT”
Fig. 12 in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 12. Zospeum neuberti Jochum & Ruthensteiner sp. nov. (NHMW Mol.Coll.Edlauer 32006). A–B. Light microscopic images of paratypes showing aperture and dorsal views and collection labels. C. Light microscopic images of holotype showing aperture and dorsal views. D–I. 3D visualizations of Micro-CT data of holotype. D. Aperture view. E. Aperture facing right view showing smooth columella. F. Apical view. G. Dorsal view showing smooth columella. H. Aperture facing left view. I. Ventral view.
Fig. 21 in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 21. Bayesian tree of the genus Zospeum Bourguignat, 1856. Node support values of both the Bayesian Inference (left) and the Maximum Likelihood analysis (right) are given. Branches are coloured to denote the informal species groups within the eastern radiation of Zospeum following Inäbnit et al. (2019). Emboldened specimen names indicate samples sequenced for this study.
Fig. 11 in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 11. Zospeum njunjicae Jochum, Schilthuizen & Ruthensteiner sp. nov. A–B. Light microscopic images of paratypes (NMBE 572616) showing aperture and dorsal views. C. Light microscopic images of holotype (NMBE 572617) showing aperture and dorsal views. D–I. 3D visualizations of X-ray microCT data of holotype (NMBE 572617). D. Aperture view. E. Aperture facing right view showing well defined lamella. F. Apical view. G. Dorsal view. H. Aperture facing left view. I. Ventral view.
Fig. 9 in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 9. Zospeum amplioscutum Jochum & Ruthensteiner sp. nov., (NHMW Mol.Coll.Edlauer 19.069) with sample labels. A. Light microscopic images of paratype (NHMW Mol.Coll.Edlauer 19.069), apertural and dorsal views. B. Light microscopic images of holotype (NHMW Mol.Coll.Edlauer 19.069), aperture and dorsal views. C–H. 3D visualizations of X-ray Micro-CT data of holotype (NHMW Mol. Coll.Edlauer 19.069). C. Aperture view. D. Aperture facing right view. E. Apical view. F. Dorsal view. G. Aperture facing left view. H. Ventral view showing coiling projecting high up on shell and peristome oblique to umbilicus.
Fig. 10 in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 10. Zospeum tumidum Jochum, Schilthuizen & Ruthensteiner sp. nov., holotype (NMBE 572615). A. Light microscopic images, showing aperture and dorsal views and TxEx Collection label. B. 3D visualizations of Micro-CT data, apical view. C. Ventral view showing deep umbilical depression. D. Aperture view. E. Aperture facing right view showing tapered columella and lamellar bulge. F. Dorsal view. G. Aperture facing left view.
Fig. 17. Z in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 17. Z. njegusiense Jochum & Ruthensteiner sp. nov., Scanning Electron Microscopy images. A. Holotype (NMBE 572639), aperture view showing subfossil shell with superficial erosion of shell layer. B. Paratype (NMBE 578378), aperture view showing close up of lamellar band on columella (Fig. C). C. Paratype (NMBE 578378), aperture view showing damaged shell and columella. D. Close up view of holotype (NMBE 572639), showing body whorl with low, irregular growth lines. E. Paratype (NMBE 578378), protoconch.
Fig. 6 in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 6. Zospeum intermedium Jochum & Ruthensteiner sp. nov. (RMNH.MOL.234132) from Gittenberger (1975). A. Light microscopic images of apertural and dorsal views. B. Sample labels. C–H. 3D visualizations of X-ray Micro-CT data. C. Aperture view. D. Aperture facing right view. E. Apical view. F. Dorsal view. G. Aperture facing right view. H. Umbilical view showing slight umbilical depression and lamella projecting from the columellar side.
Fig. 7 in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 7. Light microscopic images of shells from the caves Lipska pećina and Duboki do (Montenegro) with specimen labels. A–C. Zospeum troglobalcanicum Absolon, 1916 (MCSMNH-PMSL-Moll.-FVelkovrh 29603). D–F. Zospeum dubokidoense Jochum & Ruthensteiner sp. nov. D. Holotype (MCSMNHPMSL-Moll.-FVelkovrh 30360[spm1]). E–F. Paratypes, Duboki do, Montenegro (MCSMNH-PMSLMoll.-FVelkovrh 30360[spm2-3]).
Fig. 2. 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. 2. 3D visualizations of Micro-CT data of the lectotype of Zospeum troglobalcanicum Absolon, 1916 (NHMW Moll.Coll.Edlauer 32.749) with shell parts and terms indicated. A. Measurements include shell height (sh), shell width (sw), aperture height (ah), aperture width (aw), height of last whorl (hlw) and spire angle (SA). B. Internal view showing columella (co), lamella (la), peristome (pe) and penultimate whorl (pw). C. Apical view showing protoconch (pr), teleoconch (te) and peristome (pe). D. Ventral view showing peristome configuration (pe) parietal shield (ps) and umbilicus (um).
Fig. 4. 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. 4. 3D visualizations using Micro-CT data of shells from the caves Benetina pećina (SE Bosnia and Herzegovina) and Cetinska pećina (Montenegro). A–F. Zospeum troglobalcanicum Absolon, 1916, lectotype (NHMW Moll.Coll.Edlauer 32.749). A. Aperture view. B. Aperture facing right view. C. Apical view. D. Dorsal view. E. Aperture facing left view. F. Ventral view showing umbilical depression. G–L. Zospeum tortuosum Jochum & Ruthensteiner sp. nov., holotype (MCSMNH-PMSLMoll.-FVelkovrh 34099[spm1]). G. Aperture view. H. Aperture facing right view. I. Apical view. J. Dorsal view. K. Aperture facing left view. L. Ventral view showing callused peristome positioned mostly on top of umbilicus.
Fig. 15 in 3D X-ray microscopy (Micro-CT) and SEM reveal Zospeum troglobalcanicum Absolon, 1916 and allied species from the Western Balkans (Ellobioidea: Carychiidae)
Fig. 15. Zospeum biokovoense Jochum & Ruthensteiner sp. nov. (NHMW Mol.Coll.Edlauer 16.390). A–B. Light microscopic images showing aperture and dorsal views and collection labels. A. Juvenile shell. B. Holotype. C–H. 3D visualizations of Micro-CT data of holotype. C. Aperture view showing gnarled deformation of the columella. D. Aperture facing right view showing fat columella and lamella. E. Apical view. F. Dorsal view showing lopsided spire and incomplete lamella on top of fat columella. G. Aperture facing left view. H. Ventral view showing puckered umbilical depression.
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.
Trajectory with Overlapping Projections x-ray Computed Tomography (TOP-CT) dataset of 23 mandarins moving over a circular trajectory
<p><strong>Summary</strong></p><p>This dataset is a collection of X-ray projection images of 23 mandarins moving over a circular trajectory in such a way that the projections of multiple adjacent mandarins overlap. The dataset was acquired to test out Trajectory with Overlapping Projections x-ray Computed Tomography (TOP-CT), about which a paper is published in IEEE Transactions on Computational Imaging [Schut 2022].</p><p> </p><p><strong>Description</strong></p><p><i>Sample information</i></p><p>The samples are 23 mandarins. The first 10 are of the Nadorcott cultivar, and the remaining 13 are of the Clemenrubi cultivar. The diameter of the mandarins ranges between 50 and 58 mm. Per sample metadata can be found in the mandarin_metadata.csv file.</p><p><i>Scanner information</i></p><p>The dataset is acquired in the FleX-ray Laboratory, developed by TESCAN-XRE, located at CWI in Amsterdam. The CT scanner consists consists of a cone-beam microfocus polychromatic X-ray point source, and a 1944x1536 pixel, 14-bit, flat detector panel (Dexela1512NDT). Full details can be found in [Coban 2020].</p><p><i>Scanning geometry</i></p><p>The mandarins were moved according to a custom scanning protocol, with the intention to simulate a conveyor belt setup. A wooden disk was attached on top of the rotation stage and six evenly spaced object positions were marked on the disk at a fixed distance from the center of rotation. Pieces of cardboard tube were used as sample holders to make sure the mandarins wouldn't roll as the disk would rotate and to raise them from the disk without attenuating too much of the X-ray signal. The rotation stage was positioned in such a way that over a full rotation of the disk, each mandarin would be completely in view of the detector for more than 180 degrees of the rotation, while there would also be a position at which it would be completely out of view. An image illustrating the exact dimensions is included in mandarin_carousel_dimensions.png.</p><p>The scan was performed in phases. Every phase 400 projection images were acquired, while rotating the disk for 60 degrees. This would rotate one of the positions out of view of the scanning setup. Before the first 6 phases a mandarin was added on the position that was out of view of the setup. For the phases after that the position that would be out of view would contain a mandarin that had rotated the full circle so that mandarin was replaced with a new mandarin. At the last 6 phases there would be no new mandarins left to add so the mandarin that was out of view of the setup would only be removed. The projection images acquired from each phase were concatenated resulting in a dataset of 11200 projections. At most 5 mandarins were in view at a given time.</p><p>Note: Due to a small oversight while scanning, the 19th mandarin is not included on projections 9200-9205. This area can be masked out during reconstruction.</p><p><i>Scanning settings</i></p><p>A peak voltage of 90kV was used, the target power was set to 49.5W and the spectrum was pre-filtered using 0.1mm of copper. An exposure time of 200 ms was used for each projection. A start-stop acquisition scheme was used to minimize vibrations and to make adding and removing mandarins easier: After each projection image was acquired, the stage was rotated to a new position and the scanner was paused for 200 ms before acquiring the next projection image. Darkfield and flatfield images were acquired before and after all the mandarins were scanned using the average over 200 images. 2x2 pixel hardware binning was used and all images were cropped to a 500 pixel high region around the center, resulting in 11200 projection images of 956x500 pixels (11.1GB uncompressed). All images are stored in .tif format.</p><p><i>Reconstructing volumes</i></p><p>The repository <a href="https://github.com/D1rk123/top-ct_experiments">https://github.com/D1rk123/top-ct_experiments</a> contains code for TOP-CT simulations and reconstructions. The script mandarin_carousel_experiment.py was specifically written to reconstruct volumes for each separate mandarin from this dataset.</p><p> </p><p><strong>Research group</strong><br>These datasets are produced by the Computational Imaging group at Centrum Wiskunde & Informatica (CI-CWI) in Amsterdam, The Netherlands: <a href="https://www.cwi.nl/research/groups/computational-imaging">https://www.cwi.nl/research/groups/computational-imaging</a></p><p><strong>Contact details</strong><br>dirk [dot] schut [at] cwi [dot] nl</p><p><strong>Acknowledgments</strong><br>This work was funded by the Dutch Research Council (NWO) through the UTOPIA project (ENWSS.2018.003). The authors also acknowledge TESCAN-XRE NV for their collaboration and support of the FleX-ray laboratory.</p><p><strong>References</strong></p><p>[Schut 2022] D. E. Schut, K. J. Batenburg, R. van Liere, and T. van Leeuwen, "TOP-CT: Trajectory with Overlapping Projections X-ray Computed Tomography", 2022, IEEE Transactions on Computational Imaging<br>[Coban 2020] S. B. Coban, F. Lucka, W. J. Palenstijn, D. Van Loo, and K. J. Batenburg, "Explorative imaging and its implementation at the FleX-ray Laboratory," J. Imaging, vol. 6, no. 18, 2020, doi: 10.3390/jimaging6040018.</p><p>If you use (parts of) this data in a publication, please consider citing the first article.</p>
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>
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