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FIGURE 3 in Late Jurassic jaw bones of Halecomorph fish (Actinopterygii: Halecomorphi) studied with X-ray microcomputed tomography
FIGURE 3. Jaw bone of osteichthyan fish Furo sp. (ZPAL P.16/O-B/1): 1-2. 3-D model of 'virtual fossils'—a different view of the same specimen after digital processing and analysis of tomographic data. 4. vertical sections of Furo sp. teeth. 5. 3-D printed dentary – 'virtual fossils'. 6. specimen in piece of limestone (scale bars equal 10 mm).
FIGURE 3 in Using X-ray computed tomography analysis tools to compare the skeletal element morphology of fossil and modern frog (Anura) species
FIGURE 3. Morphological bone-to-bone comparison between the 'nominal' male (CP001) and 'actual' female (CP002) Xenopus laevis. The differences are colour-coded and show female (CP002) variance relative to the nominal bone of the male (CP001) which is depicted in the figure.
FIGURE 4 in Using X-ray computed tomography analysis tools to compare the skeletal element morphology of fossil and modern frog (Anura) species
FIGURE 4. Morphological bone-to-bone comparison between the 'nominal' Xenopus laevis (CP001) with the 'actual' fossil Xenopus sp. (ZM 71336)
FIGURE 2 in Using X-ray computed tomography analysis tools to compare the skeletal element morphology of fossil and modern frog (Anura) species
FIGURE 2. Bone cortex thickness analysis on a male Xenopus laevis (CP001) (A) and a fossil Xenopus sp. (ZM 71336) (B) depicted side by side in slice view from top view (1) and side view (3) and in a 3D colour-coded analysis (2 and 3).
FIGURE 1. A in Using X-ray computed tomography analysis tools to compare the skeletal element morphology of fossil and modern frog (Anura) species
FIGURE 1. A complete Breviceps montanus (Catalogue number ZR-050053) CT scan with segmentation of humerus and femur demonstrated.
FIGURE 14 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 14. Three-dimensional rotational model (video) of Timaniella harkeri (GSC26406). For video see palaeo-electronica.org/content/2017/1891-xmt-on-brachiopod-fossils.
FIGURE 12 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 12. XMT result of Tyloplecta nankingensis (Q-2). 1-7, serial slices in the transverse plane (from dorsal to ventral). 8-14, serial slices in the coronal plane (from posterior to anterior). 15-18, serial slices in the sagittal plane (from lateral to middle). 19-21, lateral (19), ventral (20) and dorsal (21) views of the reconstructed 3-D model (external shell). 22, ventral view of the 3-D model in transparent mode. All the slice images were obtained under false-color lookup tables (Color 1 option in DataViewer). Abbreviations: cp, cardinal process; ap, adductor platform; ms, median septum; mc, muscle scar.
FIGURE 13 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 13. Three-dimensional reconstruction model of internal shell structures of Timaniella harkeri (GSC26406). 1-6, dorsal and anterior views of the whole shell interior through posteriorly continuous rotation. 7-12, dorsal and anterior views of shell interior without spiralia through posteriorly continuous rotation.
FIGURE 11 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 11. XMT result of Meekella sangzhiensis (Q-1). 1-7, serial slices in the coronal plane (from posterior to anterior). 8-15, serial slices in the transverse plane (from ventral to dorsal). 16-21, serial slices in the sagittal plane (from lateral to middle). 22-24, lateral (22), ventral (23) and dorsal (24) views of the reconstructed 3-D model (external shell). 25, ventral view of the 3-D model in transparent mode. All the slice images were obtained under false-color lookup tables (Color 1 option in DataViewer). Abbreviation: dp, dental plate.
FIGURE 9 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 9. XMT result of Cyrtospirifer whitneyi (CD). 1-10, serial slices in the coronal plane (from posterior to anterior). 11-18, serial slices in the transverse plane (from ventral to dorsal). 19-24, serial slices in the sagittal plane (from lateral to middle). 25-28, lateral (25), ventral (26), dorsal (27) and posterior (28) views of the reconstructed 3-D model (external shell). 29, ventral view of the 3-D model in transparent mode. All the slice images were obtained under falsecolor lookup tables (Color 1 option in DataViewer). Abbreviations: dp, dental plates; tt, teeth.
FIGURE 10 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 10. XMT result of Spiriferidae gen. sp. indet. (S1). 1-8, serial slices in the coronal plane (from posterior to anterior). 9-15, serial slices in the transverse plane (from ventral to dorsal). 16-21, serial slices in the sagittal plane (from lateral to middle). 22-24, lateral (22), ventral (23) and posterior (24) views of the reconstructed 3-D model (external shell). 25, ventral view of the 3-D model in transparent mode. All the slice images were obtained under false-color lookup tables (Color 1 option in DataViewer). Abbreviation: dp, dental plates.
FIGURE 8 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 8. XMT result of Indospirifer sp. (3229). 1-8, serial slices in the coronal plane (from posterior to anterior). 9-15, serial slices in the transverse plane (from ventral to dorsal). 16-20, serial slices in the sagittal plane (from lateral to middle). 21-22, lateral (21) and ventral (22) views of the reconstructed 3-D model (external shell). 23-24, ventral (23) and ventroanterior (24) views of the 3-D model in transparent mode. All the slice images were obtained under false-color lookup tables (Color 1 option in DataViewer). Abbreviations: dp, dental plates; cp, cardinal process; hp, hinge plate; sp, spiralia.
FIGURE 5 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 5. XMT result of Cleiothyridina baracoodensis (ML32). 1-11, serial slices in the coronal plane (from posterior to anterior). 12-21, serial slices in the transverse plane (from ventral to dorsal). 22-27, serial slices in the sagittal plane (from lateral to middle). 28-31, lateral (28), ventral (29), dorsal (30) and posterior (31) views of the reconstructed 3-D model (external shell). 32, ventral view of the 3-D model in transparent mode. All the slice images were obtained under false-color lookup tables (Color 2 option in DataViewer). Abbreviations: tt, teeth; sk, socket; cf, cardinal flanges.
FIGURE 4 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 4. XMT result of Stenoscisma timorense (BS-2). 1-10, serial slices in the coronal plane (from posterior to anterior). 11-17, serial slices in the transverse plane (from ventral to dorsal). 18-22, serial slices in the sagittal plane (from lateral to middle). 23-25, lateral (23), ventral (24) and dorsal (25) views of the reconstructed 3-D model (external shell). 26, posterior view of the coronally sectioned 3-D model. 27, ventral view of the 3-D model in transparent mode. All the slice images were obtained under false-color lookup tables (Color 1 option in DataViewer). Abbreviations: sd, spondylium; tt, teeth.
FIGURE 7 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 7. XMT result of Spiriferina sp. (BS-1). 1-7, serial slices in the coronal plane (from posterior to anterior). 8-14, serial slices in the transverse plane (from ventral to dorsal). 15-19, serial slices in the sagittal plane (from lateral to middle). 20-22, lateral (20), ventral (21) and dorsal (22) views of the reconstructed 3-D model (external shell). 23, ventral view of the 3-D model in transparent mode. All the slice images were obtained under false-color lookup tables (Color 1 option in DataViewer). Abbreviations: dp, dental plates; ms, median septum; sp, spiralia; tt, teeth; cr, crus; sk, socket.
FIGURE 6 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 6. XMT result of Tylothyris transversa (TeP). 1-7, serial slices in the coronal plane (from posterior to anterior). 8-14, serial slices in the transverse plane (from ventral to dorsal). 15-19, serial slices in the sagittal plane (from lateral to middle). 20-22, lateral (20), ventral (21) and dorsal (22) views of the reconstructed 3-D model (external shell). 23, ventral view of the 3-D model in transparent mode. All the slice images were obtained under false-color lookup tables (Color 1 option in DataViewer). Abbreviation: sp, spiralia.
FIGURE 2 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 2. Thin section and cathodoluminescence (CL) photomicrographs: Indospirifer sp. (3229) (1-4), Cyrtospirifer whitneyi (CD) (5-8), Spiriferidae gen. sp. indet. (S1) (9-12), Spiriferella loveni (F8) (13-16), Meekella sangzhiensis (Q- 1) (17-18) and Tyloplecta nanjingensis (Q-2) (19-20). 1, plane-polarized light (PPL) image of infilling micrite and shell fragments scattered. 2-3, transmitted light (TL) (2) and corresponding CL (3) images of luminescent shell. 4, CL image showing slightly luminescent shell. 5-8, TL (5, 7) and CL (6, 8) images of both luminescent shell and infilling sediment. 9-10, PPL images of brachiopod shell, infilling packstone and thin silicified layer along their boundary. 11- 12, TL (11) and CL (12) images of nonluminescent shell. 13-16, TL (13, 15) and CL (14, 16) images showing a variety of shell luminescence and infilling sediment composed of calcitic skeletal grains (bryozoan in 15 and 16). 17-20, PPL (17, 19, 20) and TL (18) images of both silicified shells and infillings. Abbreviations: bs, brachiopod shell; im, infilling material; fs, fragmented shell; os, other shell material; sl, silicified layer; NL, nonluminescent; SL, slightly luminescent; L, luminescent.
FIGURE 3 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 3. XMT result of Timaniella harkeri (GSC26406). 1-10, serial slices in the coronal plane (from posterior to anterior). 11-17, serial slices in the transverse plane (from ventral to dorsal). 18-22, serial slices in the sagittal plane (from lateral to middle). 23-25, lateral (23), ventral (24) and dorsal (25) views of the reconstructed 3-D model (external shell). 26, ventral view of the 3-D model in transparent mode. All the slice images were obtained under false-color lookup tables (Color 2 option in DataViewer). Abbreviations: tt, teeth; sp, spiralia; sk, socket.
FIGURE 1 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 1. Thin section and cathodoluminescence (CL) photomicrographs: Timaniella harkeri (GSC26406) (1-4), Spiriferina sp. (BS-1) (5-8), Stenoscisma timorense (BS-2) (9-12), Cleiothyridina baracoodensis (ML32) (13-16) and Tylothyris transversa (TeP) (17-20). 1-2, transmitted light (TL) (1) and corresponding CL images (2) of nonluminescent shell and infilling sediment composed of fine sand grains. 3-4, TL (3) and CL (4) images of nonluminescent associated with partially luminescent shell in the cardinal area of dorsal valve. 5-8, TL (5, 7) and CL (6, 8) images of nonluminescent associated with partially luminescent shell and luminescent infilling cement. 9-12, TL (9, 11) and CL (10, 12) images of luminescent shell with thin silicified layers and recrystallization along inner wall of brachiopod shell. 13, plane-polarized light (PPL) image of the original infilling sediment composed of calcareous sands. 14, PPL image showing the section of infilling cement. 15-16, TL (15) and CL (16) images of slightly luminescent shell. 17, PPL image of infilling comprising lime mud, calcite cement and relatively large, radially arranged, siliceous crystals. 18-19, TL (18) and CL (19) images of nonluminescent associated with partially luminescent shell. 20, CL image showing the section of nonluminescent internal shell structure (spiralia) preserved within infilling (This structure is hardly recognized in the TL image). Abbreviations: bs, brachiopod shell; im, infilling material; sl, silicified layer; cc, calcite crystal; NL, nonluminescent; SL, slightly luminescent; L, luminescent.
Reproduction package for the paper 'Evidence for a dynamic corona in the short-term time lags of black hole X-ray binary MAXI J1820+070'
<p>This is a basic reproduction package for the paper 'Evidence for a dynamic corona in the short-term time lags of black hole X-ray binary MAXI J1820+070', Bollemeijer et al., 2024, MNRAS, 528, 558-576.</p> <ul> <li>This reproduction package aims for open science, with the internal API designation of 'Gold'.</li> <li>Authors: Niek Bollemeijer, Phil Uttley, Arkadip Basak, Adam Ingram, Jakob van den Eijnden, Kevin Alabarta, Diego Altamirano, Zaven Arzoumanian, Douglas J.K. Buisson, Andrew C. Fabian, Elizabeth Ferrara, Keith Gendreau, Jeroen Homan, Erin Kara, Craig Markwardt, Ronald A. Remillard, Andrea Sanna, James F. Steiner, Francesco Tombesi, Jingyi Wang, Yanan Wang and Abderahmen Zoghbi</li> <li>Paper DOI: https://doi.org/10.1093/mnras/stad3912</li> <li>Arxiv DOI: https://doi.org/10.48550/arXiv.2312.09835</li> <li>Published in the Monthly Notices of the Royal Astronomical Society (date of acceptance: 2023/12/12)</li> </ul> <h2>Raw Data</h2> <ul> <li>Raw event files for the described NICER observations can be obtained from the HEASARC at https://heasarc.gsfc.nasa.gov/cgi-bin/W3Browse/w3browse.pl. Select NICER as the telescope and search for MAXI_J1820+070.</li> <li>We used HEASoft v6.28 with standard reprocessing settings to obtain event lists to make light curves. See paper for details.</li> </ul> <h2>Software</h2> <ul> <li>Linux Ubuntu 22.04.</li> <li>Jupyter Notebook (7.0.7)</li> <li>Programming languages used: Python (3.12.1)</li> <li>Python packages used: numpy (1.26.3), matplotlib (3.8.2), scipy (1.12.0), astropy (6.0.0)</li> </ul> <h2>Figures and Tables</h2> <ul> <li>Figures can be reproduced from the ./figures/ folder.</li> <li>All material and data used are available as intermediate data products.</li> <li>Jupyter notebooks (.ipynb files) can be used to make all figures. Running all cells at once does not work, but you can choose the figure you want to remake and executing the relevant cells will result in those figures.</li> </ul> <h2>Intermediate data products</h2> <ul> <li>The light curve arrays that are made in the first few cells of the main Jupyter Notebook can be found in 'datafiles.zip'. </li> <li>The parameters for the Lorentzian fits of the power spectra and the grouping of different observations can be found in 'qpofitsc.txt' and 'obsidsa.txt', respectively, in the same zipped folder.</li> </ul> <h2>End-to-End analysis scripts</h2> <ul> <li>The three Jupyter notebooks that have been added can be used to make the figures and reproduce the main results of the paper. Evidence_for_a_dynamic_corona_main.ipynb is about the main body of the paper, Evidence_for_a_dynamic_corona_energy_bands.ipynb is used for a part of the Discussion involving multiple narrow energy bands and Evidence_for_a_dynamic_corona_sim.ipynb is about the simulations described in Appendix A.</li> </ul>
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.