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Cone-beam Gel phantom data for dynamic X-ray tomography
<p>The gel phantom was constructed to simulate the flow of iodine-based contrast agents in plant stems, whilst being more tolerant to the high radiation dose of X-ray tomography scanning. A thorough explanation of the phantom, its motivation and the measurement setup can be found in <a href="https://arxiv.org/abs/2003.02841">arXiv:2003.02841</a>. Attached is a brief documentation which focuses primarily on the higher dimensional 3D files and the key differences between the two data sets.</p> <p>The primary measurements consist of 17 consecutive time frames, with an initial state of no contrast agent followed by a steady increase thereof, primarily via downward diffusion into the gel body over time. Each time frame consists of 360 projections acquired with a cone-beam micro-CT scanner, resulting in a sequence of 3D cone-beam sinograms. Moreover, the first time frame is provided with higher angular sampling of 720 projections, and an additional 18th time frame with 1600 projections.</p> <p>The data set contains the following MATLAB files:</p> <ul> <li><strong>3dGelPhantomData_b4.mat</strong></li> <li><strong>3dGelPhantomData_b8.mat</strong></li> <li><strong>3dGelPhantomData_b16.mat</strong></li> <li><strong>3dGelPhantomExtraFrames_b4.mat</strong></li> <li><strong>3dGelPhantomExtraFrames_b8.mat</strong></li> <li><strong>3dGelPhantomExtraFrames_b16.mat</strong></li> </ul> <p>And a more detailed documentation: <strong>ConeBeamGelPhantomDocumentation.pdf </strong>(v1.0)</p> <p>The proper use of these files requires the <a href="https://www.astra-toolbox.com/">ASTRA Toolbox</a>, <a href="https://www.cs.ubc.ca/labs/scl/spot/">the Spot Linear-Operator Toolbox</a>, and <a href="https://www.mathworks.com/matlabcentral/fileexchange/74417-heltomo-university-of-helsinki-ct-data-toolbox">the HelTomo Toolbox</a>. In addition the operators and reconstruction algorithms provided by ASTRA for 3D geometry <strong>require CUDA capable graphics card </strong>(GPU) due to large amounts of (parallel) computations. The older <a href="https://doi.org/10.5281/zenodo.3696816">2D data set</a> provides a computationally lighter and more user-friendly starting point for inexperienced users.</p>
Dataset for "A 5.3-minute-period pulsing white dwarf in a binary detected from radio to X-rays"
<p>Photometric and spectroscopic data obtained for the manuscript "A 5.3-minute-period pulsing white dwarf in a binary detected from radio to X-rays", to be published in Nature Astronomy.</p> <p>This repository includes ultracam log files with photometry for all runs and ESO spectra.</p>
Figure 5 in X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Figure 5. The lateral wall of the braincase of Pristerodon mackayi (BP/1/2642): right prootic (blue) in (A) anterior, (B) lateral, (C) posterior, (D) ventral and (E) medial views; and left opisthotic (golden) in (F) anterior, (G) lateral and (H) posterior views. afac, articulation facet concavity; ascc, attachment of the anterior semicircular canal; boa, basioccipital sutural area; bsa, parabasisphenoid sutural area; CNV, passage of the cranial nerve five (V); eoa, exoccipital sutural area; fa, facial foramen; flo, floccular fossa; fo, fenestra ovalis; jf, jugular foramen; lscc, attachment of the lateral semicircular area; lvb, opisthotic lateral vertical buttress; osu, opisthotic posterior vertical sulcus; ovmp, opisthotic ventromedial process; pa, pila antotica; pab, prootic anterior bulge; pad, pila antotica anterior depression; pdp, prootic dorsal process; prd, prootic lateral depression; pscc, attachment of the posterior semicircular canal; ptf, posttemporal fenestra; spa, supraoccipital sutural area; vea, vestibular area; ve, vestibule. The horizontal line pattern on the prootic in (B) represents the prootic depression. The diagonal square pattern in (F) represents the articular surface of the prootic. Scale bars equal 5 mm. The upper scale bar serves for (A-E) and the lower for (F-H).
Figure 11 in X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Figure 11. Illustration of a cistecephalid species and its inferred palaeobiology. Skin texture is inspired by the naked mole-rat and the foraging behaviour typical of a fossorial taxon feeding on insects. Reconstruction credits: copyright Luzia Soares (2021).
Figure 10 in X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Figure 10. The lateral and occipital portions of the braincase of Kaaeingasaurus fossilis (GPIT-PV-117032): epipterygoid (light pink) in (A) anterior and (B) right lateral views; exoccipital (pink) in (C) anterior view; supraoccipital (dark green) in (D) anterior, (E) posterior, (F) left lateral and (G) medial views; prootic (blue) in (H) anterior, (I) lateral, (J), medial and (K) posterior views; opisthotic (golden) in (L) anterior, (M) medial and (M) posterior views. ascc, attachment of the anterior semicircular canal; cc, attachment of the crus communis; eo, exoccipital; eoc, exoccipital condyle; eocr, exoccipital descending crest; eodc, exoccipital dorsal component; epap, anteromedial angular process of the epipterygoid; epar, ascending ramus of the epipterygoid; epft, epipterygoid footplate; fa, facial foramen; flo, floccular fossa; fo, fenestra ovalis; fm, foramen magnum; ihb, impressions of the hindbrain; jf, jugular foramen; lscc, attachment of the lateral semicircular canal; nc, nuchal crest; oae, opisthotic anterior depression; od, opisthotic posterior depression; opc, opisthotic posterior crests; pa, pila antotica; pabt, prootic anterior buttress; pade, pila antotica ellipsoidal depression; pard, pila antotica anterodorsally directed ridges; pbg, prootic anterior bulge; pg, prootic anterior groove; plbt, prootic lateral vertical buttress; pmbt, prootic medial vertical buttress; prs?, prootic sinus; pscc, attachment of the posterior semicircular canal; ptf, posttemporal fenestra; pvfo, prootic vertical fossa; sacr, crests of the supraoccipital ala; saex, medial excavation of the supraoccipital lateral ala; sfo, supraoccipital posterior fossa; sap, supraoccipital anterior process of the median lobe; slr, supraoccipital lateral recess; sor, supraoccipital anterior oblique ridges; spp, supraoccipital posterior process; su, supraoccipital; tgn, passage of the cranial nerve (V); ve, vestibular area. Scale bars equal 1 mm. The first scale serves for (A-B), the second for (C-G) and the third for (H-N).
Figure 4 in X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Figure 4. The ventral and posterior walls of the braincase of Pristerodon mackayi (BP/1/2642): basioccipital (lime green) in (A) posterior, (B) dorsal, (C) ventral and (D) right lateral views; exoccipital (pink) in (E) anterior and (F) posterior views; and supraoccipital (dark green) in (G) anterior, (H) internal, (I) right lateral and (J) anterolateral views. ascc, attachment of the anterior semicircular canal; boc, basioccipital condyle; bocc, basioccipital condyle dorsal concavities; bocex, basioccipital collar-like excavation; bocf, basioccipital condyle foramina; bocr, basioccipital condyle median ridge; bomr, basioccipital median ridge; bosr, basioccipital lateral ridges; bovtr, basioccipital ventral trough; bt, basioccipital tubera; cca, attachment of the crus communis; eo, exoccipital; eoat, exoccipital anterior tuberosity; eobg, exoccipital posterior bulge; eobt, exoccipital subvertical buttress; eoc, exoccipital condyle; eodc, exoccipital dorsal component; flo, floccular fossa; fm, foramen magnum; fo, fenestra ovalis; ite, intertuberal eminence; jf, jugular foramen; ms, M-like suture between the basioccipital and exoccipital; pa, pila antotica; pbs, parabasisphenoid; pr, prootic; ptf, posttemporal fenestra; sap, supraoccipital anteriorly projected crest; sar, supraoccipital anterior recess; slr, supraoccipital lateral recess; sor, supraoccipital anterior horizontal ridges; spp, supraoccipital posterior process; su, supraoccipital; ve, vestibule. Note that the articular surface of the parabasisphenoid is black squared pattern in C. Scale bars equal 5 mm. The first scale serves for (A-D), the second for (E-F) and the third for (G-J).
Figure 2 in X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Figure 2. Comparisons of the braincase between Pristerodon and emydopoids. Pristerodon mackayi (BP/1/2642) in (A) anterior, (B) left lateral, (C) posterior and (D) ventral views. Myosaurus gracilis (BP/1/2690) in (E) anterior, (F) left lateral, (G) posterior and (H) ventral views. The Malawian cistecephalid (DMMM-PK-16-1) in (I) anterior, (J) left lateral, (K) posterior and (L) ventral views. Kaaeingasaurus fossilis (GPIT-PV-117032) in (M) anterior, (N) left lateral, (O) posterior and (P) ventral views. Dark green – supraoccipital; Purple – orbitosphenoid; Dark orange – opisthotic; Light orange – pterygoid; Green – basioccipital; Magenta – exoccipital; Cyan blue – parasphenoid rostrum; Navy blue – prootic; Aqua blue – basisphenoid; Light Rose – epipterygoid. Same color code scheme is used in the following figures.
Figure 1 in X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Figure 1. Illustration of the braincase region within the entire skull. Pristerodon mackayi (BP/1/2642) in (A) right lateral, (B) posterior and (C) ventral views. Myosaurus gracilis (BP/1/2690) in (D) right lateral, (E) posterior and (F) ventral views. The Malawian cistecephalid (DMMM-PK-16-1) in (G) left lateral and (H) posterior views. Kaaeingasaurus fossilis (GPIT-PV-117032) in (I) right lateral, (J) posterior and (K) ventral views. Note that the Malawian cistecephalid specimen is completely covered by matrix, such that a good contrast to enable the visibility of the skull was not obtained. Dark green – supraoccipital; Purple – orbitosphenoid; Dark orange – opisthotic; Light orange – pterygoid; Green – basioccipital; Magenta – exoccipital; Cyan blue – parasphenoid rostrum; Navy blue – prootic; Aqua blue – basisphenoid; Light Rose – epipterygoid.
Figure 7 in X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Figure 7. The posteroventral braincase wall of Myosaurus gracilis (BP/1/2690 and BP/1/2701a): basioccipital (lime green) in (A) posterior, (B) dorsal, (C) ventral and (D) right lateral views; the exoccipital (pink) in (E) anterior, (F) posterior, (G) dorsal and (H) ventromedial views; supraoccipital (dark green) in (I) anterior, (J) posterior, (K) ventral and (L) dorsal views; prootic (blue) in (M) anterior, (N) left lateral, (O) medial, (P) dorsal and (Q) posterior views; (R) the complete braincase of BP/1/2690 in left lateral view; opisthotic (golden) of BP/1/2690 in (S) anterior and (T) posterior views; right opisthotic of BP/1/2701a in (U) posterior view; the braincase of BP/1/2690 in (V) ventral view. ap, alar process of the prootic; ascc, attachment of the anterior semicircular canal; bo, basioccipital; boc, basioccipital condyly; bocc, basioccipital condyle concavities; bod, basioccipital ventral depression; bocdr, basioccipital condyle dorsal ridge; bomr, basioccipital median ridge; bonf, basioccipital nutritive foramina; bosr, basioccipital lateral ridges; bt, basioccipital tubera; CNV, passage of the cranial nerve five (V); eo, exoccipital; eoat, exoccipital anterior tuberosity; eoc, exoccipital condyle; eodc, exoccipital dorsal component; eopsu, exoccipital posterior sulcus; fa, facial foramen; flo, floccular fossa; fm, foramen magnum; fo, fenestra ovalis; gp, gap between the prootic and the clinoid process; hf, hypoglossal foramen; jf, jugular foramen; lscc, attachment of the lateral semicircular area; lvb, opisthotic lateral vertical buttress; ob, opisthotic body; obu, opisthotic bulges; occp, occipital pit; olc, opisthotic lateral crest; omc, opisthotic medial crest; op, opisthotic; opmb, opisthotic posteromedial buttress; osu, opisthotic posterior vertical sulcus; ovmp, opisthotic ventromedial process; pa, pila antotica; pabt, prootic anterior buttress; pbs, parabasisphenoid; ppex, prootic posterior excavation; pr, prootic; prac, pila antotica anterior crests; prmc, prootic medial crest; prpb, prootic posterior bulge; pscc, attachment of the posterior semicircular canal; pt, pterygoid; ptf, posttemporal fenestra; sac, supraoccipital semicircular crests; sap, supraoccipital anteriorly projected crest; slr, supraoccipital lateral recess; smb, supraoccipital subvertical buttress; spi, supraoccipital posterior pit; su, supraoccipital; svd, supraoccipital posterior vertical depressions; ve, vestibular area. The horizontal square pattern in (O) represents the sutural area between the prootic and supraoccipital; the horizontal line pattern in (O, Q) represents the articular surface between the prootic and the opisthotic and the oblique pattern in (O) represents the articular surface between the prootic and the parabasisphenoid. Finally, the vertical pattern in (S), represents the articular surface for the prootic on the opisthotic. Scale bars equal 5 mm. The first scale serves for (A-H), the second for (I-L), the third for (M-Q, S, T, V), the fourth for (R) and the fifth for (U).
Figure 3 in X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Figure 3. The complete and separated braincase elements of Pristerodon mackayi (BP/1/2642): orbitosphenoid in (A) anterior, (B) dorsal and (C) left lateral views; complete braincase in (D) anterior, (E) dorsal, (F) ventral, (G) occipital and (H) left lateral views; parabasisphenoid in (I) dorsal, (J) right lateral and (K) ventral views. aptr, anterior (palatal) ramus of the pterygoid; bo, basioccipital; bpdc, basisphenoidal dorsal subvertical concavity; bpt, basisphenoidal tubera; bpvsu, basisphenoidal ventral sulcus; clp, clinoid process; co, crista oesophagea; ds, dorsum sellae; eo, exoccipital; eobg, exoccipital posterior bulge; eobt, exoccipital subvertical buttress; epi, epipterygoid; fu, pterygoid anteroposterior furrow; hpl, horizontal plate; ic, internal carotid foramina; lvb, opisthotic lateral vertical buttress; mpw, mesethmoid posterior wall; obdn, the orbitosphenoid dorsal notch; obvp, orbitosphenoid medial vertical process; obw, orbitosphenoid wings; ofc, olfactory cavity; op, opisthotic; osu, opisthotic posterior vertical sulcus; ovmp, opisthotic ventromedial process; pab, prootic anterior bulge; pad, pila antotica anterior depression; pbs, parabasisphenoid; pdp, prootic dorsal process; pr, prootic; ps, parasphenoid rostrum; psgr, parasphenoid rostrum dorsal groove; pt, pterygoid; pt amp, anteromedial process of the pterygoid; pt dsu, ptergoid dorsal sulcus; ptll, pterygoid lateral lamina; ptlp, pterygoid lateral process; ptmp, pterygoid median plate; pt nt, pterygoid anteroposterior notch; ptqr, pterygoid quadrate ramus; ptvt, pterygoid ventral trench; sap, supraoccipital anteriorly projected crest; sar, supraoccipital anterior recess; slr, supraoccipital lateral recess; sor, supraoccipital anterior horizontal ridges; spp, supraoccipital posterior process; su, supraoccipital; stu, sella turcica; tse, tuberculum sellae. Scale bars equal 5 mm. The first scale serves for (A-C), the second for (D-H) and the third for (I-K).
Figure 12 in X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Figure 12. Phylogenetic results simplified to highlight Emydopoidea intra- and interrelationships. Numbers at nodes represent: Symmetric Resampling values/CG values above nodes; Bremer Support values/Relative Bremer Support values below nodes. See the Supporting Information (Figs S1–S3) for the complete tree.
Figure 9 in X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Figure 9. The anterior and ventral portions of the braincase of Kaaeingasaurus fossilis (GPIT-PV-117032): orbitosphenoid (purple) in (A) anterior, (B) dorsal and (C) left lateral views; basioccipital (lime green), parabasisphenoid (light blue) and pterygoid (yellow) in (D) dorsal, (E) left lateral and (F) ventral views; parabasisphenoid in (G) ventral view; and basioccipital in (H) posterior view. Horizontal CT-image through the parabasisphenoid and basioccipital (I). aptr, anterior (palatal) ramus of the pterygoid; bo, basioccipital; boc, basioccipital condyle; bocf, basioccipital longitudinal furrow; bolp, basioccipital lateral process; bovr, basioccipital median ridge; bovs, basioccipital vestibular space; bpt, basisphenoidal tubera; bt, basioccipital tubera; bvex, basioccipitalbasisphenoidal ventral excavation; clp, clinoid process; ds, dorsum sellae; dsu, orbitosphenoid dorsal sulcus; ic, internal carotid foramina; jf, jugular foramen; obasu, orbitosphenoid lateral sulci; obgu, orbitosphenoid dorsal gutter; obno, lateral notch; obpl, orbitosphenoid dorsal plate; obvp, orbitosphenoid medial vertical process; obw, orbitosphenoid wings; ofc, olfactory cavity; pbs, parabasisphenoid; psgr, parasphenoidal groove; pt, pterygoid; ptqr, posterior (quadrate) ramus of the pterygoid; stu, sella turcica; tra, trabecular spaces; ve, vestibule. Note that the articular surface of the exoccipital is represented by the horizontal square pattern in (D). The upper scale bar equals 5 mm and 1 mm in the lower. The upper scale serves for (A-C) and the lower for (D-H).
Figure 6 in X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Figure 6. The anterior, ventral and lateral walls of the braincase of Myosaurus gracilis (BP/1/2690 and BP/1/2701a): orbitosphenoid (purple) of BP/1/2690 in (A) anterior, (B) dorsal and (C) right lateral views; the pterygoid (yellow) of BP/1/2690 in (D) dorsal, (E) right lateral and (F) ventral views; ventral braincase floor of BP/1/2701a in (G) dorsal and (H) right lateral views; epipterygoid (pink) of BP/1/2701a in (I) anterior, (J) right lateral and (K) medial views; and the parabasisphenoid (turquoise) of BP/1/2690 in (L) dorsal, (M) left lateral and (N) ventral views. apf, pterygoid anteroposterior furrow; aptr, anterior (palatal) ramus of the pterygoid; bpt, basisphenoidal tubera; clp, clinoid process; co, crista oesophagea; ds, dorsum sellae; epar, epipterygoid ascending ramus; epdp, epipterygoid dorsal plate; epft, epipterygoid footplate; ic, internal carotid foramina; ltcr, oblique crests of the lateral wall; obacr, orbitosphenoid vertical crest; obasu, lateral sulci of the median vertical process; obdfo, orbitosphenoid dorsal fossa; obgu, orbitosphenoid gutter; obvp, orbitosphenoid vertical process; obsp, orbitosphenoid spine process; obw, orbitosphenoid wings; ofc, olfactory cavity; PRB, parasphenoid rostrum + basipresphenoid; ps, parasphenoid (light blue) rostrum; psc, parasphenoidal crests; psf, parasphenoidal foramen; pss, parasphenoidal sulcus; pt amp, anteromedial process of the pterygoid; pt gr, pterygoid dorsal groove; ptmp, pterygoid median plate; ptqr, quadrate ramus of the pterygoid; stu, sella turcica. Scale bars equal 5 mm. The first scale serves for (A-C), the second for (D-F), the third for (G-H), the fourth for (I-K) and the fifth for (L-N).
Figure 8 in X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Figure 8. The braincase of the Malawian cistecephalid DMMM-PK-16-1: ventral region of the braincase in (A) dorsal, (B) right lateral and (C) ventral views; the left exoccipital (pink) in (D) anterior and (E) posterior views; and right exoccipital (pink) in (F) medial view. Anterior wall: right prootic (blue) in (G) ventrolateral, (H) anterior; (I) lateral, (J) medial, (K) ventral and (L) posterior views. Posterior wall of the braincase: opisthotic (golden) and supraoccipital (dark green) in (M) anterior, (O) posterior and (P) right lateral views; opisthotic in (N) medial view. ap, alar process of the prootic; aptr, anterior (palatal) pterygoid ramus; ascc, attachment of the anterior semicircular canal; bo, basioccipital (lime green); boc, basioccipital condyle; bod, basioccipital ventral depression; bok, basioccipital dorsal knob; bosr, basioccipital lateral ridges; bplr, basisphenoidal lateral recess; cc, attachment of the crus communis; clp, clinoid process; co, crista oesophagea; ds, dorsum sellae; eoat, exoccipital anterior tuberosity; eodc, exoccipital dorsal component; eopsu, exoccipital posterior sulcus; epi, epipterygoid; fa, facial foramen; flo, floccular fossa; fm, foramen magnum; fo, fenestra ovalis; gap, gap between the prootic and the parabasisphenoid; hf, hypoglossal foramen; ic, internal carotid foramina; jf, jugular foramen; lscc, attachment of the lateral semicircular canal; oac, opisthotic anterior crests; oad, opisthotic anterior depression; obg, opisthotic anterior bulge; od, opisthotic posterior depression; op, opisthotic; opc, opisthotic posterior crests; opp, opisthotic posterior process; ovmp, opisthotic ventromedial process; pa, pila antotica; pbl, prootic blade-like process; pbs, parabasisphenoid; pr, prootic; ps, parasphenoid rostrum; pss, parasphenoid rostrum dorsal sulcus; pssc, attachment of the posterior semicircular canal; pt, pterygoid; ptf, posttemporal fenestra; pt ltr, pterygoid lateral trench; ptqr, pterygoid quadrate ramus; pt vsc, pterygoid ventral sulcus; sap, supraoccipital anteriorly projected crest; slr, supraoccipital lateral recess; sp, supraoccipital; ssd, supraoccipital semicircular depressions; su, supraoccipital; stu, sella turcica; tgn, passage of the trigeminal nerve (V); tmp, 'tympanic process' of Cox (1959); us, U-shaped suture; uz, unossified zone; ve, vestibular area. Scale bars equal 5 mm, except for (G) which equals to 1 mm. The first scale serves for (A-C), the second for (D-F), the third for (G), the fourth for (H-L) and the fifth for (M-P).
Extended X-ray absorption spectroscopy using an ultrashort pulse laboratory-scale laser-plasma accelerator
<p>The data contained in this repository was used in the production of the publication "Extended X-ray absorption spectroscopy using an ultrashort pulse laboratory-scale laser-plasma accelerator"</p>
Supplementary Documents for Manuscript 'Investigating the use of two-dimensional OSL laser scanning instruments and energy-dispersive x-ray spectroscopy for OSL exposure dating'
<p>Appendix Data for Manuscript 'Investigating the use of two-dimensional OSL laser scanning instruments and energy-dispersive x-ray spectroscopy for OSL exposure dating' - with added "Readme's" for relevant databases.</p>
MESA input and software files for: 'The imprint of convection on Type I X-ray bursts: Pauses in photospheric radius expansion lightcurves'
<p>Inlists, input models, and other machinery needed to reproduce results in "The imprint of convection on Type I X-ray bursts: Pauses in photospheric radius expansion lightcurves". Includes data files (profiles and histories, and also some movies) for the main "Schwarzschild" run.</p> <p>MESA version: 15140</p> <p>See the README.md for instructions on how to run.</p> <p> </p>
Supplementary material S1. Henoticus groehni sp. nov., holotype, No. 5087 [GPIH], X-ray micro-CT volume rendering of the habitus.
<p>Supplementary material S1 in paper: Bukejs A., Lyubarsky G.Yu., Alekseev V.I. The oldest fossil species of the genus <em>Henoticus</em> Thomson (Coleoptera: Cryptophagidae) from Eocene Baltic amber. <em>Historical Biology</em>.</p> <p> </p>
Supplementary material S2. Henoticus groehni sp. nov., holotype, No. 5087 [GPIH], X-ray micro-CT volume rendering of the habitus without legs.
<p>Supplementary material S2 in paper: Bukejs A., Lyubarsky G.Yu., Alekseev V.I. The oldest fossil species of the genus Henoticus Thomson (Coleoptera: Cryptophagidae) from Eocene Baltic amber. Historical Biology.</p> <p> </p>
Fiber Orientation Estimation from X-ray Dark Field Images of Fiber Reinforced Polymers using Constrained Spherical Deconvolution: Data
<p>The data was simulated in GATEv8.0. The macro's and other files for the simulation can be found in the folders: Sim_50_40, Sim80_60 and Sim90_70. Here, the different files to perform the simulation are given, as well as the output data, found in the folders Flats and Projs (flatfields and projections) in the form of a csv-file. The csv-file contains 5000 rows (one for each image), and each row contains a flattened 450x450 image.</p> <p>The files for visualization of the fiber directions are given in the folder MRtrix. This folder contains the reconstructed scatter magnitudes and their respective directions in a mat-file. On this set of directions the constrained spherical deconvolution is applied using the sf_dirs.mif, sf_mask.mif, sf_response.mif and data.mif files. This returns the orientation density function in each voxel as output (odf_csd_14.mif). An alternative approach is performing a Funk-Radon transform on the coefficients of the scatter function (data_coeffs_10.mif) to obtain odf_frt_10.mif.</p> <p>Using a peak finding algorithm the fiber orientations are extracted from these odf-files and written to peaks_x.mif files, with or without a threshold (10% of largest amplitude).</p>
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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
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.