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FIGURE 2 in Pushing the limits of neutron tomography in palaeontology: Three-dimensional modelling of in situ resin within fossil plants

FIGURE 2. Austrosequoia novae-zeelandiae (Ettingshausen, 1887) Mays et al., 2017, PL1227. 1) Transverse section of a partially exposed, desiccated ovulate cone. 2) Neutron tomographic reconstruction largely encapsulated in sedimentary matrix, white indicates high neutron attenuation, oblique-transverse view. 3) Volume rendering of neutron tomographic reconstruction, RNA = Relative Neutron Attenuation, grid texture on RNA spectrum indicates relative transparency, regions of highest neutron attenuation represent in situ resin within cone axis and minor enclaves of resin near the distal ends of the bract-scale complexes, desiccation exhibited by large gaps in coalified organic remains (blue/green), oblique-transverse view. 4) Greyscale histogram from neutron tomographic reconstruction of PL1227 (16-bit) these values represent the neutron attenuation of the reconstructed volume, colours and transparency textures as per Figure 2.3, threshold values presented in Table 2, the spectrum has been cropped at the extremes for this graphical representation. See Appendix for an animation of the virtually extracted specimen illustrated in Figure 2.3.

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FIGURE 1. 1 in Pushing the limits of neutron tomography in palaeontology: Three-dimensional modelling of in situ resin within fossil plants

FIGURE 1. 1) Map of eastern Zealandia including New Zealand and the Chatham Islands, grey areas = emergent, grey outline = 2000 m isobath, boxed area is displayed in Figure 1.2. 2) Map of the Chatham Islands, grey areas = emergent, boxed area is displayed in Figure 1.3. 3) Geological map of the Waihere Bay area, northwest Pitt Island, fossil locality recorded in this study is indicated, age estimates from the following sources: Tupuangi Formation (Mildenhall, 1994; Mays and Stilwell, 2013), Kahuitara Tuff (Mildenhall, 1994; Stilwell, 1998), other estimates (Campbell et al., 1993; Panter et al., 2006). Modified from figures 1 and 3 of Mays et al. (2015b) with permission.

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FIGURE 3 in Pushing the limits of neutron tomography in palaeontology: Three-dimensional modelling of in situ resin within fossil plants

FIGURE 3. Artist's reconstruction of ovuliferous cone and fertile shoot of Austrosequoia novae-zeelandiae (Ettingshausen, 1887) Mays et al., 2017, artist: Mali Moir.

FIGURE 5 in A novel application of the white light/fringe projection duo: recovering high precision three-dimensional images from fossils for the digital preservation of morphology

FIGURE 5. Processed views of a fossil sample acquired by the optical FPP system OTY. Each view is re-oriented 60º degrees with respect to the prior. Where: "a" indicates a zone that has no information at 60º in this stage of the process and will be corrected with the information of the next view, as is shown in "b".

FIGURE 3 in A novel application of the white light/fringe projection duo: recovering high precision three-dimensional images from fossils for the digital preservation of morphology

FIGURE 3. Magnitude maps of the sample obtained every 60º for 8 and 128 pixels/period. The images show the resolution and detail levels given the number of fringes projected over the sample. The measurements' accuracy of surface and depth depends on the number of projected fringes, which include as many as the system can display (8 pixels/period for each fringe in this case). When the acquisition of details is difficult, a wider fringe is required (based on our sample size, we used 128 pixels).

FIGURE 1 in A novel application of the white light/fringe projection duo: recovering high precision three-dimensional images from fossils for the digital preservation of morphology

FIGURE 1. Optical set up specifications for fringe projection profilometry (FPP) used in this study for the recovery of a 3-D image of a hemimandible sample.

FIGURE 7 in A novel application of the white light/fringe projection duo: recovering high precision three-dimensional images from fossils for the digital preservation of morphology

FIGURE 7. Examples of analyses that can be performed with the obtained data from the fossils: 1) denoting the relief (emboss filter), 2) detecting edges and transitions (sobel filter), 3) study of the roughness and waviness of a sample (topography filter).

FIGURE 2 in A novel application of the white light/fringe projection duo: recovering high precision three-dimensional images from fossils for the digital preservation of morphology

FIGURE 2. Flowchart of the 'OTY' procedure employed in this study, where: α = angle (60º in this case), * = MBE algorithm (Gutiérrez-García et al., 2013), and ** = Goldstein algorithm. OTY: name given to the white light system together with the phase shifting algorithm filter, based on the fact that it was developed for use on Ototylomys samples (see main text).

FIGURE 6. Full 3-D in A novel application of the white light/fringe projection duo: recovering high precision three-dimensional images from fossils for the digital preservation of morphology

FIGURE 6. Full 3-D image of the reconstructed fossil after merging all the six views. 1) Cloud of points, 2) Final mesh.

FIGURE 4 in A novel application of the white light/fringe projection duo: recovering high precision three-dimensional images from fossils for the digital preservation of morphology

FIGURE 4. Process applied to recover the topography of the fossil sample. Where: 1) image captured by the CCD of the fringe projection on the sample, 2) wrapped phase obtained of the 8 frames after applying the MBE filter, 3) unwrapped phase map, 4) phase carrier compensation, and 5) surface of one of the views of the fossil recovered.

Fig. 17 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 17. Idealized and representing two extremes, three−dimensional models of septal microstructures in corals with fibrous skeletal tissue. First extreme model (A), shows perfect continuity between organo−mineral phases of dRAF and TD regions, whereas the second extreme model (B) shows consistent discontinuity of these phases in longitudinal, perpendicular to septal plane section. Real specimens (e.g., Figs. 3E–H, 5B) usually have some regions with dRAF and TD layers continuing, and some parts where these layers discontinue. Left to A, longitudinal section through RAF plane. Septal surfaces in the RAF zone may have "microcrystalline" texture (if a snapshot were taken during formation of the mineral phase); "microcrystals" represent exposed fiber tips (fasciculi of Wise 1972) of organic−depleted zones (circle on right of A).

Fig. 16. The rugosan Endotheciumdecipiens Koker, 1924 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 16. The rugosan Endotheciumdecipiens Koker, 1924. Here re−illustrated from Schindewolf's (1942: fig. 7). Lower Upper Permian (Basleo−Schichten), Basleo, Timor. "Transverse" section of corallum (A) with septa in axial region (B) showing alternation of layers of fibers (white) and areas infilled by dark (?iron−manganese rich) minerals (see also footnote 2). TLM view.

Fig. 15. A. Pachythecalis major Cuif, 1975, ZPAL H.23 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 15. A. Pachythecalis major Cuif, 1975, ZPAL H.23/10. Triassic, Lower Norian. Alakir Çay,Turkey. Transverse polished corallite in TLM (A1); enlargement of dRAF (A2). A3. Transverse polished pachytheca in TLM; fibers show faint regular (ca. 7 µm) alternations of lighter and darker zones. B. Zardinophyllum zardini Montanaro−Gallitelli, 1975. Triassic (Middle Carnian), San Cassiano Beds, Alpe di Specie, Dolomiti (Italy). Completely smooth RAF of septum in distal view, IPUM11 (B1, SEM). B2. Transverse, polished and etched septum (ZPALH.23/11); note fissure in dRAF region (arrow), more or less regular discontinuities in arrangement of pachytheca fibers (arrows), and secondary, probably biogenic deposits filling up the calice (marked transparent dark grey). All coralla with still preserved aragonitic mineralogy.

Fig. 14. Pachysolenia cylindrica Cuif, 1975 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 14. Pachysolenia cylindrica Cuif, 1975, ZPALH. XXI/4. Triassic, Lower Norian. Alakir Çay,Turkey. A–C. Complementary regions of transversely sectioned and polished pachytheca: TLM image (A), greyscale Sr (B) and Mg (C) mapping acquired on the electron microprobe by wavelength−dispersive techniques; darker areas equal very low concentration whereas lighter areas equal slightly higher concentrations. Sr (in B) shows enrichment, at least in some regions (arrows) where Mg (in C) appears depleted. Sr mapping of diagenetically non−altered fibrous parts of coralla of extant corals (not illustrated here) invariably shows nearly homogenous distribution of this element. D. TLM view of longitudinally sectioned pachytheca and septum; part of the preserved septum encircled and enlarged in E to show "non−trabecular" nature of dRAF. F. Transverse polished section of pachytheca in TLM; fibers show faint regular 5–8 µm alternations of lighter and darker zones. G. Homogenous septal dRAF zone in SEM view of transversely polished and etched section. H. Transverse polished and etched section of pachytheca (SEM); fibrous skeleton shows negative and positive etching relief (at ca. 5–8 µm distance).

Fig. 13.Stylophyllumparadoxum Frech, 1890, NHMW 1982 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 13.Stylophyllumparadoxum Frech, 1890, NHMW 1982/57/100, corallum with aragonitic mineralogy still preserved. Triassic, Rhaetian, Fischerwiese, Northern Calcareous Alps, Austria. A, B. Transverse section of septa with concentric arrangement of fibers within septal spines (B, enlargement). C–F. Longitudinal sections crossing centers of septal spines; domed, successive layers of aragonite fibers (darker) separated by lighter "voids" infilled by spar (see D, F enlargements). Except for regular voids in spine centers, there is no difference in organization of superimposed layers of fibers within septal spine. All TLM micrographs.

Fig. 5. Flabellum chunii Marenzeller, 1904 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 5. Flabellum chunii Marenzeller, 1904. Recent, Great Meteor Seamount, SEAMOUNT2 (1993), DW 152 (January 11, 1993), 30°02.00'N, 28°22.10'W, 470 m. A. Septa and inner side of wall (A1) thickened by fibers arranged in scale−like units (A2, enlargement); ZPALH.23/2/1. B. Marginothecal wall sectioned longitudinally (large white arrow); layers of successive growth increments (dRAF) continue in wall "stereome", i.e.,TD (small white arrows); ZPAL H.23/2/2. C. Septum longitudinally sectioned in RAF plane. Dissolved or etched components of RAF form narrow "strands" (C2 enlargement); ZPALH.23/2/3. D. Transverse polished and etched section of septum; dRAF zone composed of neighboring dCRA (D1) is from both sides covered with layers of TD fibers (D2) which direction conform to that of scale−like units (i.e., semi−parallel to RAF); ZPALH.23/2/4. All SEM; growth direction within skeletal element i ndicated by black arrow in B.

Fig. 12. Undetermined conophylliid. ZPALH.23 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 12. Undetermined conophylliid. ZPALH.23/9. Triassic (Middle Carnian), San Cassiano Beds, Alpe di Specie, Dolomiti (Italy), corallum still wi th aragonitic mineralogy preserved. B. Transverse polished section of corallite in TLM (A); enlarged portions of longitudinally sectioned septa with regular growth increments of fibers (B). C. Longitudinally polished and etched section of septum with fibers regularly tapered (SEM). D. Transverse, polished and etched septum (SEM) with dCRA ("center of calcification", arrows). E. Septum longitudinally sectioned in dCRA region with domed, successive layers of fibers and occasional (arrow) larger voids between them.

Fig. 10 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 10. Galaxea fascicularis (Linnaeus, 1767); ZPAL H.23/7 (originally NMNH 90860 lot). Recent, North Pacific Ocean, Central Philippines (southern parts of islands), coll. J.B. Steere. A. Transverse polished section of septum in TLM; note dRAF in lower right corner (brown "calcification center") and regular growth increments of TD fibers (red arrows). B. SEM of transverse (slightly oblique) polished and etched section of septum; fibers adjacent to dRAF (bottom) show regular tapering periods at ca. 2–3 µm: red arrows). Oblique sectioned dRAD, with dissolved/etched inner components have crescent appearance. C. Transverse polished (slightly oblique) section of septum, TLM view; dRAF show brownish coloration; borders between bundles of fibers only gently outlined (white arrows). D. The same septal fragment as C, stained with acridine orange in MFM view; dRAF exhibit light, green−yellow fluorescence, whereas borders between bundles of fibers (arrows) emphasize greenish fluorescence.

Fig. 9 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 9. Galaxea fascicularis (Linnaeus, 1767); ZPAL H.23/7 (originally NMNH 90860 lot). Recent, North Pacific Ocean, Central Philippines (southern parts of islands), collection J.B. Steere. A, B. Morphology of distal septal edge (A) and septal flank spine (B). Note "Persian lamb" texture of skeletal surface (as shown by these fasciculi). C, D. Transverse section of polished and etched septum. Arrow in enlarged (D) fragment (general view in C) shows "blurry", probably organic material in dCRA and adjacent, radiating TD fibers (ca. 3–5 µm growth increments). E, F. Septum longitudinally sectioned in RAF plane; note dissolved/etched dRAF components in longitudinal "strand" (F enlargement). All are SEM.

Fig. 4. Stephanocyathuspaliferus Cairns 1977. ZPALH.23 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 4. Stephanocyathuspaliferus Cairns 1977. ZPALH.23/1. Locality data as in Fig. 1. A–C. AFM (contact mode): height—2D projection (A), phase (B), and height—3D projection (C) images of 5 m2 polished (not etched) septum sectioned in RAF plane; AFM tip was placed in dRAF "strand" region as seen in etched sections (Fig. 3C). D, E. AFM (tapping mode) height—2D projection (D) and phase (E) images of spherical bodies seen on the bottom of dRAF "strand".