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Figures 78-80 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 78-80 Quasicalathus conservans sp. nov., volume rendering of the holotype using different grey scales of the Amira software. 78. Dorsal aspect; 79. Left lateral aspect (aed – aedeagus); 80. Ventral aspect; the aedeagus (highlighted by red colour) was separated by the segmentation function of Amira software.
Figures 52-57 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 52-57 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimen "Groehn 7889". 52. Head, ventral aspect (the arrows point to the insertions of the setae near base of mentum tooth and on submentum); 53. Abdomen, left lateral aspect (the arrows point to the insertions of the setae on ventrites IV, V, and VI); 54. Metacoxal area (the arrows point to the insertions of the coxal setae); 55. Apical gonocoxites, ventral aspect; 56. Apical gonocoxites, dorsal aspect; 57. Gonocoxites and remains of the bursa copulatrix (the latter was highlighted by red colour using the segmentation function of Amira software). Abbreviations: at – apical tooth of retinacle; kes – metathoracic katepisternum; cx – metacoxa; cxp – metacoxal plate; des – dorsal ensiform setae; ep – elytral epipleuron; fm – metafemur; gu – gula; mdl – left mandible; gx1 – basal gonocoxite; gx2 – apical gonocoxite; mdr – right mandible; mo – molar; mt – mentum; sp – sensory pit; tr – metatrochanter; ves – ventral ensiform setae; v3, v4, v5, v6 – ventritres III, IV, V, VI.
Figures 73-77 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 73-77 Quasicalathus agonicollis sp. nov., volume rendering of specimen "GZG 16188". 73. Dorsal aspect; 74. Basal portion of pronotum and anterior part of elytra (right side of body; the arrows point to the insertions of the pronotal basolateral seta and the parascutellar seta); 75. Prosternum with basal portion of prolegs; 76. Left apical gonocoxite, ventral aspect; 77. Gonocoxites, ventral aspect. Abbreviations: cx – procoxa; des – dorsal ensiform setae; fm – profemur; gx1 – basal gonocoxite; gx2 – apical gonocoxite; hm – humerus; pst – prosternum; sc – scutellum; sps – setae of sensory pit; tr – protrochanter; ves – ventral ensiform setae.
Figures 13-17 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 13-17 Quasicalathus elpis (Ortuño and Arillo 2009), light microscopic images of specimens "CCHH 952" (13–15.) and "OSAC 269" (16, 17.). 13. Dorsal view of body; 14. Pronotum and anterior part of elytra showing the markedly concave basal margin and projected humeri (the white arrows point the insertion pores of the parascutellary setae); 15, 17. General view of the amber pieces; 16. Posterior part of left elytron (the white arrow points to the insertion of the discal seta).
Figures 18-24 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 18-24 Quasicalathus, light microscopic images of Q. elpis Ortuño & Arillo, 2009 (18–20.) and Q. agonicollis sp. nov. (21–24.). 18. General view of the amber piece "MAIG 76" (only that part of the large amber piece bearing the Quasicalathus fossil is shown; the fossil is widely covered by milky coating); 19. General view of the two fragments of specimen "GZG 16185"; the left one bears only the negative imprint of the left elytra on the inclusion wall; 20. Right anterior part of body of specimen "GZG 16185" showing part of head, pronotum and humerus; 21, 22. General view of the amber piece "GZG 16188" (21. With fossil in dorsal view; 22. In ventral view); 23. Anterior part of specimen "GZG 16188"; 24. Head of specimen "GZG 16188". Abbreviations: a1–a6 – antennomeres 1–6; as – anterior supraorbital seta; bs – pronotal laterobasal seta; ms – pronotal lateral seta; ps – posterior supraorbital seta.
Figures 58-60 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 58-60 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of the dorsal aspects of specimens "Groehn 7962" (58.), "CCHH 952" (59.), and "OSAC 265" (60.).
Figures 65-72 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 65-72 Quasicalathus agonicollis sp. nov., volume rendering of the holotype using different grey scales of the Amira software. 65. Dorsal aspect (the negative imprint of the fossil on the inclusion wall is shown); 66. Basal portion of pronotum and anterior part of elytra (positive of the fossilized beetle is shown; the arrows point to the insertions of the pronotal basolateral setae and the parascutellar setae); 67. Metacoxa (the arrows point to the insertions of the three coxal setae each side); 68–71. Aedeagus in dorsal aspect (68.), Right lateral aspect (69.), Ventral aspect (70.), Left lateral aspect (71.); The remains of the parameres are coloured (red: left paramere; green: right paramere); 72. left lateral aspect of beetle body; the aedeagus (highlighted by red colour) was separated by the segmentation function of Amira software. Abbreviations: bb – basal bulb of aedeagal median lobe; hm – humerus; os – distal ostium of median lobe; sc – scutellum; tl – terminal lamella of median lobe.
Figures 1-5 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 1-5 Quasicalathus elpis (Ortuño and Arillo 2009), light microscopic images of specimens "Groehn 4879" (1–3.) and "Groehn 7814" (4, 5.). 1, 5. General view of the amber pieces; 2. Ventral side of head (the white arrow points to the mentum tooth; note that the mentum is somewhat detached from the head capsule); 3. Pronotum and anterior part of elytra showing the markedly concave basal margin and projected humeri; 4. Right lateral view of body.
Figures 25-30 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 25-30 Quasicalathus agonicollis sp. nov., light microscopic images of specimen "GZG 16188" (25–26.) and the holotype (28–30.). 25. Posterior part of pronotum and anterior part of elytra, right side; 26. Anterior part of fifth interval of left elytra showing microsculpture; 27. Posterior part of elytra (the arrows point to the insertions of the discal setae); 28. General view of the amber piece; 29. Right dorsal view of beetle body (the arrow points to the insertion of the discal seta on left elytron); 30. Left ventral view. Abbreviations: bs – insertion of the pronotal laterobasal seta; hm – humerus; m – mite (syninclusion).
Text-fig. 5. Anacardiaceae (a–m), Burseraceae (n–q). Scale bars = 1 cm. a–f: Pentoperculum sp. a–c: USNM PAL 772360. a: Lateral view of endocarp, apex up; three germination valves visible, the central clearly displaying the bipartite nature of the valve, reflected light, palladium coated. b: Apical view displaying six locules, with two preserved germination valves at the lower left, reflected light, palladium coated. c: Basal view of the endocarp, the locules suggested by swellings; note point of attachment, micro-CT scan surface rendering. d–f: Pentoperculum sp. USNM PAL 772359, reflected light, palladium coated. d: Lateral view of a probable 6-loculed endocarp, apex up; a single intact germination valve in the center, displaying the central lineation that divides it in two. e: Apical view; two bi-partite germination valves are visible, indicated by arrows to the middle cleavage line of two of the valves. f: Basal view, the locules suggested by the undulations in the margin. g–i: Indet. Spondioideae. USNM PAL 772358, reflected light, palladium coated. g: Lateral view of multi-locular endocarp, apex up. h: Apical view showing finely punctuate surface and peripheral locule cavities. i: Basal view. j–m: Cf. Pleiogynium USNM PAL 772357. j: Lateral view of the multi-locular endocarp, apex up; note intact germination valve on left and exposed locule facing the viewer, micro-CT scan surface rendering. k: Lateral view, rotated about 30° from (j), showing three exposed locules, reflected light, palladium coated; note bipartite locule lining at center. l: Apical view of the multilocular endocarp; the locule with intact germination valve at the upper right, reflected light, palladium coated. Arrows to each locule. m: Basal view showing central point of attachment and prominent radiating ridges aligned with the locules, micro-CT scan surface rendering. n–q: Canarium, USNM PAL 772361. Scale bar = 1 cm. n: Lateral view of endocarp directly facing one germination valve flanked by two strong ridges; apex up; specimen coated in sodium nitrate and photographed by R. A. Scott. o: Lateral view facing one of the three pronounced ridges, flanked to the left and right by two germination valves; apex up. p: Apical view displaying the three strong ridges, arching over the apex and flanking three deep embayments, covered with germination valves. q: Basal view, the three ridges being less pronounced. o–q: Reflected light, palladium coated. in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 5. Anacardiaceae (a–m), Burseraceae (n–q). Scale bars = 1 cm. a–f: Pentoperculum sp. a–c: USNM PAL 772360. a: Lateral view of endocarp, apex up; three germination valves visible, the central clearly displaying the bipartite nature of the valve, reflected light, palladium coated. b: Apical view displaying six locules, with two preserved germination valves at the lower left, reflected light, palladium coated. c: Basal view of the endocarp, the locules suggested by swellings; note point of attachment, micro-CT scan surface rendering. d–f: Pentoperculum sp. USNM PAL 772359, reflected light, palladium coated. d: Lateral view of a probable 6-loculed endocarp, apex up; a single intact germination valve in the center, displaying the central lineation that divides it in two. e: Apical view; two bi-partite germination valves are visible, indicated by arrows to the middle cleavage line of two of the valves. f: Basal view, the locules suggested by the undulations in the margin. g–i: Indet. Spondioideae. USNM PAL 772358, reflected light, palladium coated. g: Lateral view of multi-locular endocarp, apex up. h: Apical view showing finely punctuate surface and peripheral locule cavities. i: Basal view. j–m: Cf. Pleiogynium USNM PAL 772357. j: Lateral view of the multi-locular endocarp, apex up; note intact germination valve on left and exposed locule facing the viewer, micro-CT scan surface rendering. k: Lateral view, rotated about 30° from (j), showing three exposed locules, reflected light, palladium coated; note bipartite locule lining at center. l: Apical view of the multilocular endocarp; the locule with intact germination valve at the upper right, reflected light, palladium coated. Arrows to each locule. m: Basal view showing central point of attachment and prominent radiating ridges aligned with the locules, micro-CT scan surface rendering. n–q: Canarium, USNM PAL 772361. Scale bar = 1 cm. n: Lateral view of endocarp directly facing one germination valve flanked by two strong ridges; apex up; specimen coated in sodium nitrate and photographed by R. A. Scott. o: Lateral view facing one of the three pronounced ridges, flanked to the left and right by two germination valves; apex up. p: Apical view displaying the three strong ridges, arching over the apex and flanking three deep embayments, covered with germination valves. q: Basal view, the three ridges being less pronounced. o–q: Reflected light, palladium coated.
FIGURE A2 in Testing the impact of two key scan parameters on the quality and repeatability of measurements from CT scan data
FIGURE A2. Box and whisker plots of impact of the number of x-ray radiographs averaged per view on the signal-to-noise ratio of (1) the background, and (2) the shell material. The background SNR increases with increased number of averages because this random noise is averaged out as more x-ray radiographs are collected. The material SNR decreases with increasing number of x-ray radiographs which suggest the data are noisy and the noise is not random. Data are available in Appendix 4.
FIGURE A1.1 in Testing the impact of two key scan parameters on the quality and repeatability of measurements from CT scan data
FIGURE A1.1. Variation in total shell volume with exposure time when different surface determination calculation methods are used. Three scans were interpreted for this graph, one from each exposure time.
FIGURE 3. A in Testing the impact of two key scan parameters on the quality and repeatability of measurements from CT scan data
FIGURE 3. A schematic diagram of CT data (A) and slices of CT data collected as part of the scan parameter experiment (B-E). The presented data are sections through the central whorl of a shell of the pteropod Limacina retroversa. The green line in part 1 represents the boundaries of the shell material. The yellow box represents the same region on each scan. The white material is shell, the dark grey material is organic matter, and the black material is air. The difference among the three materials is clearer at the longer scan times (D and E) than the shorter scan times (B and C), making it easier to separate digitally and quantify the different materials.
Fig. 2 in An XXL-CT-scan of an XXL Tyrannosaurus rex skull
Fig. 2. Mechanical setup of the XXL-CT system.
Fig. 8 in An XXL-CT-scan of an XXL Tyrannosaurus rex skull
Fig. 8. Extraction of the brain segment (blue) for further processing to a 3D-printer.
Fig. 1. Linac bremsstrahlung spectra for 6 and 9 in An XXL-CT-scan of an XXL Tyrannosaurus rex skull
Fig. 1. Linac bremsstrahlung spectra for 6 and 9 MeV electrons.
Fig. 7 in An XXL-CT-scan of an XXL Tyrannosaurus rex skull
Fig. 7. Virtual excavation of the skull by removing the sandstone matrix and support structures
Fig. 3 in An XXL-CT-scan of an XXL Tyrannosaurus rex skull
Fig. 3. Preparation of the skull at the excavation site.
RibSeg Dataset and Strong Point Cloud Baselines for Rib Segmentation from CT Scans
<p>Manual rib inspections in computed tomography (CT) scans are clinically critical but labor-intensive, as 24 ribs are typically elongated and oblique in 3D volumes. Automatic rib segmentation methods can speed up the process through rib measurement and visualization. However, prior arts mostly use in-house labeled datasets that are publicly unavailable and work on dense 3D volumes that are computationally inefficient. To address these issues, we develop a labeled rib segmentation benchmark, named RibSeg, including 490 CT scans (11,719 individual ribs) from a public dataset. For ground truth generation, we used existing morphology-based algorithms and manually refined its results. Then, considering the sparsity of ribs in 3D volumes, we thresholded and sampled sparse voxels from the input and designed a point cloud-based baseline method for rib segmentation. The proposed method achieves state-of-the-art segmentation performance (Dice<span class="math-tex">\(\approx95\%\)</span>) with significant efficiency (<span class="math-tex">\(10\sim40\times\)</span> faster than prior arts). The RibSeg dataset, code, and model in PyTorch are available at <a href="https://github.com/M3DV/RibSeg">https://github.com/M3DV/RibSeg</a>.</p> <p> </p> <p><strong>Note:</strong> This repository provides rib segmentation ("RibFrac31-rib-seg.nii.gz") and centerline ("RibFrac31-rib-cl.nii.gz") <em>annotations</em> for 490 cases in RibFrac dataset. Please download the corresponding CT <em>images </em>("RibFrac31-image.nii.gz") at <a href="https://ribfrac.grand-challenge.org/">https://ribfrac.grand-challenge.org/</a> (1-click registration is needed via <em>"Join"</em>).</p>
Fig. 24 in Morphology of the Braincase in the Cretaceous Hybodont Shark Tribodus limae (Chondrichthyes: Elasmobranchii), Based on CT Scanning
Fig. 24. Close-up of lateral basicranial foramina in Tribodus limae (UERJ-PMB-40). Scale bar is 1 cm.
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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)
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
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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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