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52 results for “micro CT scan”
Text-fig. 1. Diplopanax cacaoides (ZENKER) comb. nov. a–d: [Holotype of Mastixia cantia E.REID et M.CHANDLER, V.22953]. a: Lateral view of longitudinally broken specimen, reflected light. b–d: Surface renderings from micro-CT data. b: Lateral view of longitudinal fracture surface. c: Same specimen rotated to show external surface. d: Enlargement of lower half from (a, b), reflected light. e, f: Specimen figured originally as a paratype of M. cantia, V.22954 (Reid and Chandler 1933: pl. 25, fig. 3), reflected light. e: Ventral view with much of the endocarp wall fallen away exposing smooth convex ventral surface of locule cast. f: Transversely fractured surface, showing thick wall of the endocarp, and dehiscence plane leading to the left limb of the locule. g: Transversely sectioned, laterally compressed specimen from Miocene of Wiesa, Germany for comparison, Senckenberg Museum, SM.B. 21034/I. h–j: Digital transverse sections from micro-CT data of the Holotype V.22953. h: Transverse fracture surface from (b), showing curved locule and zone of weakness defining the germination valve (arrow), reflected light. i: Same orientation with clear demarcation of the separation plane of the germination valve (arrow), digital section from micro-CT scan. j: Enlargement from (h). Scale bars 5 mm. in Mastixioid Fruits (Cornales) From The Early Eocene London Clay Flora: Morphology, Anatomy And Nomenclatural Revision
Text-fig. 1. Diplopanax cacaoides (ZENKER) comb. nov. a–d: [Holotype of Mastixia cantia E.REID et M.CHANDLER, V.22953]. a: Lateral view of longitudinally broken specimen, reflected light. b–d: Surface renderings from micro-CT data. b: Lateral view of longitudinal fracture surface. c: Same specimen rotated to show external surface. d: Enlargement of lower half from (a, b), reflected light. e, f: Specimen figured originally as a paratype of M. cantia, V.22954 (Reid and Chandler 1933: pl. 25, fig. 3), reflected light. e: Ventral view with much of the endocarp wall fallen away exposing smooth convex ventral surface of locule cast. f: Transversely fractured surface, showing thick wall of the endocarp, and dehiscence plane leading to the left limb of the locule. g: Transversely sectioned, laterally compressed specimen from Miocene of Wiesa, Germany for comparison, Senckenberg Museum, SM.B. 21034/I. h–j: Digital transverse sections from micro-CT data of the Holotype V.22953. h: Transverse fracture surface from (b), showing curved locule and zone of weakness defining the germination valve (arrow), reflected light. i: Same orientation with clear demarcation of the separation plane of the germination valve (arrow), digital section from micro-CT scan. j: Enlargement from (h). Scale bars 5 mm.
Text-fig. 4. Mastixia cf. oregonensis (R.A.SCOTT) TIFFNEY et HAGGARD from the London Clay, originally included within the concept of M. cantiensis. a–c: V. 22960(1). a: Transverse fracture, showing c-shaped locule, dorsal infold, and sculptured endocarp, reflected light. b: Transverse digital section from micro-CT scan data. c: Surface view of ribbed endocarp extracted from micro-CT data. d: Transverse fracture, reflected light, V. 22955 (originally illustrated in pl. 25, fig. 4 of Reid and Chandler 1933). e, f: Transverse physical section, V. 22963(2) showing U-shaped locule and longitudinal dorsal infold. g–i reflected light. g: Detail from left of (d). h, i: Detail from right of (f). Scale bars 5 mm in (a–f), 1 mm in (g–i). in Mastixioid Fruits (Cornales) From The Early Eocene London Clay Flora: Morphology, Anatomy And Nomenclatural Revision
Text-fig. 4. Mastixia cf. oregonensis (R.A.SCOTT) TIFFNEY et HAGGARD from the London Clay, originally included within the concept of M. cantiensis. a–c: V. 22960(1). a: Transverse fracture, showing c-shaped locule, dorsal infold, and sculptured endocarp, reflected light. b: Transverse digital section from micro-CT scan data. c: Surface view of ribbed endocarp extracted from micro-CT data. d: Transverse fracture, reflected light, V. 22955 (originally illustrated in pl. 25, fig. 4 of Reid and Chandler 1933). e, f: Transverse physical section, V. 22963(2) showing U-shaped locule and longitudinal dorsal infold. g–i reflected light. g: Detail from left of (d). h, i: Detail from right of (f). Scale bars 5 mm in (a–f), 1 mm in (g–i).
Text-fig. 3. Juglandaceae. Carya (a–x). Scale bars = 1 cm. a–e: USNM PAL 772346. Micro-CT scan surface rendering. a, b: Lateral, c: apical, d: basal views. e: Virtual equatorial transverse section. f–n: USNM PAL 772347. f: Lateral view, reflected light, showing path of saw cut for transverse section of (i). g: Basal view, reflected light. h: Apical view, micro-CT surface rendering. i: Physical transverse section displaying locule and cellular preservation of parts of wall. j–n: Virtual sections from micro-CT scan data. j: Transverse section at apical 1/3 of nut. Note narrow lacunae (arrows). k: Longitudinal section parallel to primary septum, traversing one of the cotyledon lobes and showing secondary septum at base. l: Longitudinal section in plane at right angles to (k) in plane of primary septum, showing divergent placental bundles arising from base of nut (arrows). m: Equatorial transverse section showing two lobes of locule separated by primary septum. n: Transverse section near base of nut showing primary and secondary septa, creating four basal lobes of locule; note diverging placental bundles (arrows). o–x: USNM PAL 772351. o: Lateral view of broken nut with exposed locule cast, reflected light. p: Same orientation of nut, micro-CT surface rendering. q: Same specimen lateral view, rotated 90° from (p), micro-CT surface rendering. r: Apical view, reflected light. s–x: Virtual sections from micro-CT in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 3. Juglandaceae. Carya (a–x). Scale bars = 1 cm. a–e: USNM PAL 772346. Micro-CT scan surface rendering. a, b: Lateral, c: apical, d: basal views. e: Virtual equatorial transverse section. f–n: USNM PAL 772347. f: Lateral view, reflected light, showing path of saw cut for transverse section of (i). g: Basal view, reflected light. h: Apical view, micro-CT surface rendering. i: Physical transverse section displaying locule and cellular preservation of parts of wall. j–n: Virtual sections from micro-CT scan data. j: Transverse section at apical 1/3 of nut. Note narrow lacunae (arrows). k: Longitudinal section parallel to primary septum, traversing one of the cotyledon lobes and showing secondary septum at base. l: Longitudinal section in plane at right angles to (k) in plane of primary septum, showing divergent placental bundles arising from base of nut (arrows). m: Equatorial transverse section showing two lobes of locule separated by primary septum. n: Transverse section near base of nut showing primary and secondary septa, creating four basal lobes of locule; note diverging placental bundles (arrows). o–x: USNM PAL 772351. o: Lateral view of broken nut with exposed locule cast, reflected light. p: Same orientation of nut, micro-CT surface rendering. q: Same specimen lateral view, rotated 90° from (p), micro-CT surface rendering. r: Apical view, reflected light. s–x: Virtual sections from micro-CT
Text-fig. 7. Cornacaeae (a–j), Icacinaceae (k–o). a–e: Mastixia. USNM PAL 772364. Scale bar = 1 cm. a: Lateral view of eroded endocarp – the opposite side being missing and the endocarp broken near its mid point, reflected light, palladium coated. b–e: Micro-CT scan surface renderings. b: Rotated 90° from the view in (a). c: Rotated 90° from the view in (b). d: Rotated 90° from (c), exhibiting the damaged "back" face of the endocarp. e: Axillary view of the endocarp; the opposite end missing as apparent in (d). f–j: Cf. Nyssa. DMNH EPI.47808. Scale bar = 1 cm. Micro-CT scan surface renderings. f: Intact face of the endocarp; note ridges and "apical" point. g: Eroded (?gnawed; note horizontal grooving) opposite face of the endocarp. h: Lateral view of the endocarp, eroded/gnawed face to left. i: Apical view, eroded/gnawn portion below. j: Basal view of endocarp. k–o: Iodes DMNH-EPI.47807. Micro-CT scan surface renderings. Scale bar = 1 cm. k: Face view of endocarp. l: Opposite face of endocarp. m: Lateral view demonstrating the compressed nature of the endocarp, note thickened suture marking the probable track of the primary bundle. n: Apical view, primary bundle trace to right. o: Basal view, primary bundle trace to right. in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 7. Cornacaeae (a–j), Icacinaceae (k–o). a–e: Mastixia. USNM PAL 772364. Scale bar = 1 cm. a: Lateral view of eroded endocarp – the opposite side being missing and the endocarp broken near its mid point, reflected light, palladium coated. b–e: Micro-CT scan surface renderings. b: Rotated 90° from the view in (a). c: Rotated 90° from the view in (b). d: Rotated 90° from (c), exhibiting the damaged "back" face of the endocarp. e: Axillary view of the endocarp; the opposite end missing as apparent in (d). f–j: Cf. Nyssa. DMNH EPI.47808. Scale bar = 1 cm. Micro-CT scan surface renderings. f: Intact face of the endocarp; note ridges and "apical" point. g: Eroded (?gnawed; note horizontal grooving) opposite face of the endocarp. h: Lateral view of the endocarp, eroded/gnawed face to left. i: Apical view, eroded/gnawn portion below. j: Basal view of endocarp. k–o: Iodes DMNH-EPI.47807. Micro-CT scan surface renderings. Scale bar = 1 cm. k: Face view of endocarp. l: Opposite face of endocarp. m: Lateral view demonstrating the compressed nature of the endocarp, note thickened suture marking the probable track of the primary bundle. n: Apical view, primary bundle trace to right. o: Basal view, primary bundle trace to right.
Text-fig. 10. Carpolithes (a–j). a–d: Carpolithes sp. 10. USNM PAL 772375. Scale bar = 5 mm, reflected light, palladium coated. a: Lateral view of one face of structure; note adherent mineral material. Longitudinal groove is to right. b: Lateral view of one edge of the structure. c: Opposite view from (b), note groove in upper half of the specimen, facing viewer. d: Apical view. e–j: Carpolithes sp. 11. USNM PAL 772376. Scale bar = 5 mm, micro-CT scan surface views. e: Structure in face view showing central protuberance. f: Same, lateral view. g: Opposite face from (e). h: Opposite face from (f). i: View from one end. j: View from opposite end from (i). in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 10. Carpolithes (a–j). a–d: Carpolithes sp. 10. USNM PAL 772375. Scale bar = 5 mm, reflected light, palladium coated. a: Lateral view of one face of structure; note adherent mineral material. Longitudinal groove is to right. b: Lateral view of one edge of the structure. c: Opposite view from (b), note groove in upper half of the specimen, facing viewer. d: Apical view. e–j: Carpolithes sp. 11. USNM PAL 772376. Scale bar = 5 mm, micro-CT scan surface views. e: Structure in face view showing central protuberance. f: Same, lateral view. g: Opposite face from (e). h: Opposite face from (f). i: View from one end. j: View from opposite end from (i).
Text-fig. 6. Cornaceae. Alangium (a–e), Mastixia (f–r). a–e: Alangium, DMNH EPI.47806. Scale bar = 1 cm. b, e: Reflected light, palladium coated. a, c, d: Micro-CT scan surface rendering. a: Locule cast, face view of slightly larger locule. b: Face view of slightly smaller locule. c: Lateral view of the endocarp, the slightly enlarged left carpel separated from the smaller carpel by a longitudinal septal groove; the faint pitting in the groove suggestive of the septal vasculature. d, e: Views of either end of the endocarp, illustrating the size difference between the two carpels and the pitting in the septal groove suggestive of the septal vasculature. f–k: Mastixia USNM PAL 772362. Scale bar = 1 cm. f, g, j, k: reflected light, palladium coated; h, i: micro-CT scan surface rendering. f: Lateral view of endocarp, inferred dorsal germination valve groove facing the viewer. Note irregular, rugose, longitudinal ridges. g: Lateral view of endocarp, inferred germination valve with median longitudinal groove to left. h: Lateral view of endocarp reoriented with the same longitudinal groove to the right. i: Lateral view, rotated to ventral surface. j: View of one end of the endocarp, germination valve groove up. k: Opposite end view, with prominent radial ridges and intervening grooves, germination valve groove up. l–r: Mastixia USNM PAL 772363. Scale bar = 1 cm. l: View of one face of endocarp, displaying a groove that may represent the surficial expression of the dorsal infold of a Mastixia-like germination valve. Surface badly eroded, reflected light, palladium coated. m: Opposite face of endocarp displaying extensive erosion and a central hole interpreted as feeding damage. n: Lateral view; m, n micro-CT scan surface renderings. o: A view of one end, displaying the prominent groove, reflected light, palladium coated. p: Opposite end to (o). q: View as in (o); p, q micro-CT scan surface renderings. r: Virtual transverse section showing curved locule (arrows). in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 6. Cornaceae. Alangium (a–e), Mastixia (f–r). a–e: Alangium, DMNH EPI.47806. Scale bar = 1 cm. b, e: Reflected light, palladium coated. a, c, d: Micro-CT scan surface rendering. a: Locule cast, face view of slightly larger locule. b: Face view of slightly smaller locule. c: Lateral view of the endocarp, the slightly enlarged left carpel separated from the smaller carpel by a longitudinal septal groove; the faint pitting in the groove suggestive of the septal vasculature. d, e: Views of either end of the endocarp, illustrating the size difference between the two carpels and the pitting in the septal groove suggestive of the septal vasculature. f–k: Mastixia USNM PAL 772362. Scale bar = 1 cm. f, g, j, k: reflected light, palladium coated; h, i: micro-CT scan surface rendering. f: Lateral view of endocarp, inferred dorsal germination valve groove facing the viewer. Note irregular, rugose, longitudinal ridges. g: Lateral view of endocarp, inferred germination valve with median longitudinal groove to left. h: Lateral view of endocarp reoriented with the same longitudinal groove to the right. i: Lateral view, rotated to ventral surface. j: View of one end of the endocarp, germination valve groove up. k: Opposite end view, with prominent radial ridges and intervening grooves, germination valve groove up. l–r: Mastixia USNM PAL 772363. Scale bar = 1 cm. l: View of one face of endocarp, displaying a groove that may represent the surficial expression of the dorsal infold of a Mastixia-like germination valve. Surface badly eroded, reflected light, palladium coated. m: Opposite face of endocarp displaying extensive erosion and a central hole interpreted as feeding damage. n: Lateral view; m, n micro-CT scan surface renderings. o: A view of one end, displaying the prominent groove, reflected light, palladium coated. p: Opposite end to (o). q: View as in (o); p, q micro-CT scan surface renderings. r: Virtual transverse section showing curved locule (arrows).
Text-fig. 8. Carpolithes (a–t). a–e: Carpolithes sp. 1. USNM PAL 772366. Scale bar = 1 cm. a: Lateral view of endocarp, note two longitudinal ridges. b: Lateral view of endocarp rotated 90° from (a), note single lateral ridge in center, a, b reflected light, palladium coated. c: Lateral view, Micro-CT scan surface rendering. d: View of rounded end of the endocarp, reflected light, palladium coated. e: View of the opposite (pointed) end of the endocarp, note split; reflected light, palladium coated. f–j: Carpolithes sp. 2. USNM PAL 772367. Scale bar = 5 mm. f: Lateral view, base down; note raphe-like structure (arrow), reflected light, palladium coated. g: Lateral view, the raphe-like structure extending vertically from the base. h: Lateral view, rotated 90° from (g). i: Lateral view, the opposite face to that in (h). j: Basal view, raphe-like structure running from the center to the right of the image. g–j: CT scan surface renderings. k–o: Carpolithes sp. 3 USNM PAL 772368. Scale bar = 5 mm. k: Ventral view of the specimen, note flared apical extension, reflected light, uncoated. l: Dorsal view illustrating the flared apical extension, rotated 180o from (k). m: Lateral view rotated 90° from that in (l). n: Apical view, the apical extension with central pore (arrow) and a clear lineation running down the side to the top of the image. o: Basal view. l–o: Micro-CT scan surface renderings. p–t: Carpolithes sp. 4. USNM PAL 772369. Scale bar = 3 mm. p: Basal view illustrating the concentric rings of radiating possible cells surrounding a central depression. q: Lateral view, base down, note possible cellular pattern. r: Lateral view, rotated 180° from (q), base down; p–r: reflected light, palladium coated. s, t: Basal and lateral views, micro-CT scan surface renderings. in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 8. Carpolithes (a–t). a–e: Carpolithes sp. 1. USNM PAL 772366. Scale bar = 1 cm. a: Lateral view of endocarp, note two longitudinal ridges. b: Lateral view of endocarp rotated 90° from (a), note single lateral ridge in center, a, b reflected light, palladium coated. c: Lateral view, Micro-CT scan surface rendering. d: View of rounded end of the endocarp, reflected light, palladium coated. e: View of the opposite (pointed) end of the endocarp, note split; reflected light, palladium coated. f–j: Carpolithes sp. 2. USNM PAL 772367. Scale bar = 5 mm. f: Lateral view, base down; note raphe-like structure (arrow), reflected light, palladium coated. g: Lateral view, the raphe-like structure extending vertically from the base. h: Lateral view, rotated 90° from (g). i: Lateral view, the opposite face to that in (h). j: Basal view, raphe-like structure running from the center to the right of the image. g–j: CT scan surface renderings. k–o: Carpolithes sp. 3 USNM PAL 772368. Scale bar = 5 mm. k: Ventral view of the specimen, note flared apical extension, reflected light, uncoated. l: Dorsal view illustrating the flared apical extension, rotated 180o from (k). m: Lateral view rotated 90° from that in (l). n: Apical view, the apical extension with central pore (arrow) and a clear lineation running down the side to the top of the image. o: Basal view. l–o: Micro-CT scan surface renderings. p–t: Carpolithes sp. 4. USNM PAL 772369. Scale bar = 3 mm. p: Basal view illustrating the concentric rings of radiating possible cells surrounding a central depression. q: Lateral view, base down, note possible cellular pattern. r: Lateral view, rotated 180° from (q), base down; p–r: reflected light, palladium coated. s, t: Basal and lateral views, micro-CT scan surface renderings.
Text-fig. 9. Carpolithes (a–r). a–d: Carpolithes sp. 5. USNM PAL 772370. Scale bar = 5 mm, reflected light, palladium coated. a: Lateral view of seed, apex up, possible raphe descending from apex toward viewer. b: Lateral view of seed, apex up, possible raphe on right. c: Lateral view, opposite side, apex up, possible raphe on left. d: Apical view, note central pit with raphe descending towards bottom margin. e–h: Carpolithes sp. 6. USNM PAL 772371. Scale bar = 5 mm. e: Basal view illustrating depression and keel in plane of bisymmetry, reflected light, palladium coated. f–h: Micro-CT scan surface rendering. f: Lateral view showing relatively smooth rounded surface. g: Specimen rotated 180° from (f), surface partially eroded. h: Longitudinal view, showing median keel. i–m: Carpolithes sp. 7 USNM PAL 772372. Scale bar = 5 mm. i: View of intact face of globose fruit, possible apical constriction at top. j: Lateral view, intact surface to right, possible apical constriction at top, both micro-CT scan surface renderings. k: Apical view. l: Face view illustrating the mineral filling and the fine, radiating structure of the fruit wall on the left and right margins, both reflected light, palladium coated. m: Closeup of the cellular layer on the left of (l), micro-CT scan surface rendering. n–p: Carpolithes sp. 8. USNM PAL 772373. Scale bar = 3 mm, reflected light, palladium coated. n: Lateral view of pyrene-like structure, one ridge running vertically in the center of view, the other two forming the left and right margins. o: Lateral view of pyrene-like structure, ridge in (n) on the left. p: End-on view illustrating one convex, one concave, and one relatively flat to very slightly concave face. q, r: Carpolithes sp. 9 USNM PAL 772374. Scale bar = 5 mm, reflected light, palladium coated. q: Exterior of the smooth broken half-sphere. r: Interior of the broken half-sphere. in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 9. Carpolithes (a–r). a–d: Carpolithes sp. 5. USNM PAL 772370. Scale bar = 5 mm, reflected light, palladium coated. a: Lateral view of seed, apex up, possible raphe descending from apex toward viewer. b: Lateral view of seed, apex up, possible raphe on right. c: Lateral view, opposite side, apex up, possible raphe on left. d: Apical view, note central pit with raphe descending towards bottom margin. e–h: Carpolithes sp. 6. USNM PAL 772371. Scale bar = 5 mm. e: Basal view illustrating depression and keel in plane of bisymmetry, reflected light, palladium coated. f–h: Micro-CT scan surface rendering. f: Lateral view showing relatively smooth rounded surface. g: Specimen rotated 180° from (f), surface partially eroded. h: Longitudinal view, showing median keel. i–m: Carpolithes sp. 7 USNM PAL 772372. Scale bar = 5 mm. i: View of intact face of globose fruit, possible apical constriction at top. j: Lateral view, intact surface to right, possible apical constriction at top, both micro-CT scan surface renderings. k: Apical view. l: Face view illustrating the mineral filling and the fine, radiating structure of the fruit wall on the left and right margins, both reflected light, palladium coated. m: Closeup of the cellular layer on the left of (l), micro-CT scan surface rendering. n–p: Carpolithes sp. 8. USNM PAL 772373. Scale bar = 3 mm, reflected light, palladium coated. n: Lateral view of pyrene-like structure, one ridge running vertically in the center of view, the other two forming the left and right margins. o: Lateral view of pyrene-like structure, ridge in (n) on the left. p: End-on view illustrating one convex, one concave, and one relatively flat to very slightly concave face. q, r: Carpolithes sp. 9 USNM PAL 772374. Scale bar = 5 mm, reflected light, palladium coated. q: Exterior of the smooth broken half-sphere. r: Interior of the broken half-sphere.
Fig. 8 in Impact of increasing morphological information by micro-CT scanning on the phylogenetic placement of Darwin wasps (Hymenoptera, Ichneumonidae) in amber
Fig. 8 Holotype of Rhyssa gulliveri sp. nov. A Habitus of specimen, lateral view. B Rugae dorsally on mesoscutum. C Face, anterior view, partially hidden by spider inclusion and milky coatings. D Face, more laterally with visible mandibles. E First tergite on metasoma, lateral view. F Head and mesoscutum, dorsal view. G Interpretative drawing with an additional drawing of the propodeum and T1 in dorsal view, where photos and micro-CT scan were used as templates. Scale bar A: 2 mm, B and C: 1 mm, D: upper 1 mm, lower 2 mm
Fig. 7 in Impact of increasing morphological information by micro-CT scanning on the phylogenetic placement of Darwin wasps (Hymenoptera, Ichneumonidae) in amber
Fig. 7 Holotype of Firkantus freddykruegeri gen. et sp. nov. A Habitus of specimen, lateral view. B Anterior view of face, right side with facial structures indicated. C Fore wing with folds indicating wing venation. D Anterior part of metasoma, dorsal view. E Posterior part of metasoma, with parameters and aedeagus. F Interpretative drawing with an additional drawing of the propodeum and T1 in dorsal view, where photos and micro-CT scan were used as templates. Scale bar A: 1 mm, B: 0.5 mm, F: lower 1 mm, right 0.5 mm
Fig. 3 in Impact of increasing morphological information by micro-CT scanning on the phylogenetic placement of Darwin wasps (Hymenoptera, Ichneumonidae) in amber
Fig. 3 RoguePlot placement of Pimplinae fossil Firkantus freddykruegeri gen. et sp. nov. before and after micro-CT scanning. The plots include all branches from the majority-rule consensus tree where the attachment probability was higher than 1%. A Firkantus freddykruegeri gen. et sp. nov. with colours indicating newly revealed body characteristics. Blue colouration represents newly added measurements; orange highlights either newly coded characters or characters where states could be reduced after the CT scan. B Placement before CT scanning. C Placement after CT scanning
Fig. 6 in Impact of increasing morphological information by micro-CT scanning on the phylogenetic placement of Darwin wasps (Hymenoptera, Ichneumonidae) in amber
Fig. 6 Holotype of Triclistus levii sp. nov. A Partial fore wing. B Metasoma, posterior end with the parameres. C Habitus of specimen, lateral view. D Head and mesoscutum, dorsal view. E Head. F Interpretative drawing with an additional drawing of the propodeum and T1, in dorsal view, where photos and micro-CT scan were used as templates. Scale bars A: 1 mm, B: 0.5 mm C: 1 mm F: bottom 1 mm, top right 0.5 mm
Fig. 9 in Impact of increasing morphological information by micro-CT scanning on the phylogenetic placement of Darwin wasps (Hymenoptera, Ichneumonidae) in amber
Fig. 9 Holotype Magnocula sarcophaga gen. et sp. nov. A Habitus of specimen, ventral view. B Habitus of holotype, lateral view. CT scan of C head and mesoscutum in dorsal view, D face in anterior view, and E last tergites with ovipositor and sheaths. F Photo of a partial fore wing, in top left is T2 with its rugopunctate to striate structure. G Interpretative drawing with an additional drawing of the propodeum and T1 in dorsal view, where photos and micro-CT scan were used as templates. Scale bar A: 1 mm, F: 0.5 mm G: lower 1 mm, right 0.5 mm
Fig. 2 in Impact of increasing morphological information by micro-CT scanning on the phylogenetic placement of Darwin wasps (Hymenoptera, Ichneumonidae) in amber
Fig. 2 RoguePlot placement of Metopiinae fossil Triclistus levii sp. nov. before and after micro-CT scanning. The plots include all branches from the majority-rule consensus tree where the attachment probability was higher than 1%. A Triclistus levii sp. nov. with colours indicating newly revealed body characteristics after the CT scan. Blue colouration represents newly added measurements; orange highlights either newly coded characters or characters where states could be reduced after the CT scan. B Placement before CT scanning. C Placement after CT scanning
Fig. 5 in Impact of increasing morphological information by micro-CT scanning on the phylogenetic placement of Darwin wasps (Hymenoptera, Ichneumonidae) in amber
Fig. 5 RoguePlot placement of Phygadeuontinae fossil Magnocula sarcophaga gen. et sp. nov. before and after micro-CT scanning. The plots include all branches from the majority-rule consensus tree where the attachment probability was higher than 1%. A Magnocula sarcophaga gen. et sp. nov. with colours indicating newly revealed body characteristics. Blue colouration represents newly added measurements; orange highlights either newly coded characters or characters where states could be reduced after the CT scan. B Placement before CT scanning. C Placement after CT scanning
Fig. 4 in Impact of increasing morphological information by micro-CT scanning on the phylogenetic placement of Darwin wasps (Hymenoptera, Ichneumonidae) in amber
Fig. 4 RoguePlot placement of Rhyssinae fossil Rhyssa gulliveri sp. nov. before and after micro-CT scanning. The plots include all branches from the majority-rule consensus tree where the attachment probability was higher than 1%. A Rhyssa guliveri sp. nov. with colours indicating newly revealed body characteristics. Blue colouration represents newly added measurements; orange highlights either newly coded characters or characters where states could be reduced after the CT scan. B Placement before CT scanning. C Placement after CT scanning
Micro-CT scans, whole-test meshes, and internal chamber segments of planktonic foraminifera for three-dimensional analysis of inter- and intra-specific variation in ontogenetic growth trajectories
<p> </p> <p>Here, we release tomographic reconstructions of 42 planktonic foraminifera from plankton tows and sediment traps, along with meshes and shrinkwrap meshes the whole tests and internal meshes of segmented chambers. Shrinkwrap meshes are test meshes that have been modified to close all pores and apertures in the test. Additionally, we have provided sample metadata for each specimen and volumetric measurements for the tests and chambers. This dataset was used in a study of ontogenetic growth in planktonic foraminifera and its variation within and among species.</p> <p> The CT-scans and reconstructions were obtained at Naturalis Biodiversity Center in Leiden, the Netherlands with a Zeiss Xradia 520 Versa micro-CT scanner. The meshes and segments were created at Yale University.</p> <ol> <li>Sample_Metadata.csv: Spreadsheet containing information on the sampling localities and dates for all specimens.</li> <li>Scan_data.csv: Spreadsheet containing metadata for all micro-CT scans including current strength, pixel size, voltage, image height, image width, and the number of images taken.</li> <li>Whole_Test_Measurements.csv: Spreadsheet containing measurements of linear dimensions (axis1, axis2, axis 3), total number of chambers, calcite test volume, calcite test surface area, shrinkwrap volumes, and and shrinkwrap surface areas for all specimens.</li> <li>Chamber_Measurements.csv: Spreadsheet containing measurements of individual internal chamber segments, including position from the final chamber (F-chamber), position from the first chamber (Chamber), volume, and surface area.</li> <li>CT_Scan_Stacks.zip: reconstructed micro-CT image stacks (.tif files) for each specimen.</li> <li>Meshes.zip: Meshes of the test calcite, the shrinkwrap, and the internal chamber segments for each specimen (.stl 3D mesh files). Regular test meshes are named with the format “SampleID.stl”, and shrinkwrap meshes are named “SampleID-WRAP.stl”. Chamber meshes are named “SampleID-CH#.stl” and “SampleID-CH#-Wrap.stl”. Chambers are numbered in relation to their position from the final chamber, with “CH1” being the final chamber and “CH2” being the penultimate chamber.</li> </ol> <p>This data is described and analyzed in the manuscript “Three-Dimensional Analysis of Inter- and Intraspecific Variation in Ontogenetic Growth Trajectories of Planktonic Foraminifera” submitted to the journal <em>Marine Micropaleontology.</em></p>
micro CT scan of Ice core, publication DOI:10.1109/TGRS.2023.3334867
<p>The dataset is used in the paper:</p> <p><strong>Bagherzadeh, Faramarz, et al. "Ice-Core Micro-CT Image Segmentation With Deep Learning and Gaussian Mixture Model." <em>IEEE Transactions on Geoscience and Remote Sensing</em> 61 (2023): 1-11.</strong><br><strong>DOI:10.1109/TGRS.2023.3334867</strong></p> <p><br>Polar ice cores 2D images of Micro CT scans that could be used for training and testing a deep neural network for image segmentation. This dataset is connected with the corresponding paper:<br>Title: "Ice Core micro-CT Image Segmentation with Deep Learning and Gaussian Mixture Model"</p> <p>There are mainly 3 specimens from Polar regions (snow, firn, and bubbly ice) with 60-micron resolution and a corresponding ground truth per input which was derived from a higher-resolution image with the methodology explained in the article.</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>
3D Mapping from micro-CT scans of Equisetum arvense Rhizome
<p>These two animation (rotating 360 degrees) show <strong>1)</strong> a full 10cm x 5cm core of <em>E. arvense</em> L., and <strong>2)</strong> a section of nodal root whorls with good-quality mapping of parent roots, but no lateral root detail. These images were mapped by Conor Haynes-Mannering from micro-CT scans taken in the Hounsfield Lab (Sutton Bonnington campus, UK), supervised by Craig Sturrock and Brian Atkinson.</p>
ScienceDex guides
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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.