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opencc-by-4.0May 2024View details →

Multienergy Fan Beam Computed Tomography Dataset of a Bird Chest Imaged with 3 Different X-ray Spectra

Summary This dataset is a collection of X-ray projection data of a biological imaging phantom (a bird chest) imaged in an X-ray microtomography scanner, using three different X-ray spectra. The dataset also includes a metadata file for each of the scans, specifying the scan geometry and other important scan parameters, as well as photographs and example reconstructions. The dataset is designed for use in algorithm development for multienergy computed tomography.   Description Sample Information The sample is the chest of a common quail (Coturnix coturnix) bird obtained frozen from a local supermarket. The chest section of the frozen bird was removed using a handsaw, and left to melt and settle in a sample holder before imaging. Scanner The measurement data were acquired using an X-ray microtomography scanner in the University of Helsinki Micro-CT Laboratory. The scanner uses cone beam geometry and it is equipped with an end-window tube with a tungsten target. Scan Settings The dataset consists of three consecutive scans made using identical geometry but different X-ray spectra and detector exposure times. For each scan, 720 X-ray projections were acquired using an angle increment of 0.5 degrees. Multiple frames were averaged for each projection in order to increase signal-to-noise ratio. The scan geometry and the energy-specific settings are summarized in the following two tables. Table 1. Imaging geometry used for collecting the data. <table> <tbody> <tr> <td>Parameter</td> <td>Value</td> </tr> <tr> <td>Focus-center distance</td> <td>252 mm</td> </tr> <tr> <td>Focus-detector distance</td> <td>420 mm</td> </tr> <tr> <td>Geometric magnification</td> <td>5/2</td> </tr> <tr> <td>Detector pixel size</td> <td>0.200 mm</td> </tr> <tr> <td>Effective pixel size</td> <td>0.120 mm</td> </tr> <tr> <td>Projection size</td> <td>552 x 576 pixels</td> </tr> <tr> <td>Angular range</td> <td>360'</td> </tr> <tr> <td>#projections</td> <td>720</td> </tr> </tbody> </table> Table 2. Energy-specific settings used for collecting the data. <table> <tbody> <tr> <td>Energy label</td> <td>U (kV)</td> <td>Filtration</td> <td>I (μA)</td> <td>Exposure time (ms)</td> <td>Frame averaging</td> </tr> <tr> <td>E1</td> <td>50</td> <td>None</td> <td>300</td> <td>125</td> <td>4</td> </tr> <tr> <td>E2</td> <td>80</td> <td>1 mm Al</td> <td>180</td> <td>125</td> <td>4</td> </tr> <tr> <td>E3</td> <td>120</td> <td>0.5 mm Cu</td> <td>120</td> <td>250</td> <td>4</td> </tr> </tbody> </table> Data Post-Processing Before the scans were made, a dark current image and flat-field image were acquired for each scan setting. During the scans, dark current subtraction and flat-field correction were automatically applied to the X-ray projections by the measurement software. Data Contents This dataset contains the following files: <ul> <li>The raw projection data (.tif format) for each scan and a metadata file (.txt format) describing the measurement setup, with formatting that is both human-readable and machine-readable.</li> <li>Pre-created 2D sinograms for each energy level. The sinograms have been created from the central plane of the cone beam, which reduces to fan beam geometry. The sinograms are stored in Matlab's .mat file format in data structures which also contain metadata on the measurement.</li> <li>Photographs taken during the measurement process.</li> <li>Example filtered backprojection (FBP) reconstructions of the central plane of the phantom for each energy. The reconstructions were computed using the  Phoenix datos|x CT software provided with the microtomography scanner</li> </ul>   Research Group This dataset was produced by the Inverse Problems research group at the Department of Mathematics and Statistics at the University of Helsinki, Finland (<a href="https://www.helsinki.fi/en/researchgroups/inverse-problems">https://www.helsinki.fi/en/researchgroups/inverse-problems</a>) in collaboration with the Computational Physics and Inverse Problems research group at the University of Eastern Finland, Finland (<a href="https://sites.uef.fi/inverse">https://sites.uef.fi/inverse</a>) and the X-ray Laboratory at the Department of Physics at the University of Helsinki, Finland (<a href="https://www.helsinki.fi/en/researchgroups/x-ray-laboratory">https://www.helsinki.fi/en/researchgroups/x-ray-laboratory</a>).   Previous Use This dataset has been used in the following publications: Jussi Toivanen, Alexander Meaney, Samuli Siltanen, Ville Kolehmainen. Joint reconstruction in low dose multi-energy CT. Inverse Problems and Imaging, 2020, 14(4): 607-629. doi: <a href="https://doi.org/10.3934/ipi.2020028" target="_blank" rel="noopener">10.3934/ipi.2020028</a>. E. Cueva, A. Meaney, S. Siltanen, M. J. Ehrhardt. Synergistic multi-spectral CT reconstruction with directional total variation. Philos Trans A Math Phys Eng Sci. 2021 Aug 23;379(2204):20200198. doi: <a href="https://doi.org/10.1098/rsta.2020.0198">10.1098/rsta.2020.0198</a>.   Additional Links To get started with the data, we recommend looking at the HelTomo toolbox, specifically created for working with CBCT data collected by the Inverse Problems research group, and available at <a href="https://se.mathworks.com/matlabcentral/fileexchange/74417-heltomo-helsinki-tomography-toolbox">https://se.mathworks.com/matlabcentral/fileexchange/74417-heltomo-helsinki-tomography-toolbox</a>.   Acknowledgements We wish to thank laboratory engineer Heikki Suhonen for his guidance and assistance in conducting the measurements.   Contact Details For more information or guidance in using these datasets, please contact alexander.meaney [at] helsinki.fi.

Figure 1 in The first extinct species of Acritus LeConte, 1853 (Histeridae: Abraeinae) from Eocene Baltic amber: a microscopic beetle inclusion studied with X-ray micro-computed tomography

Figure 1. Photomicrographs of Acritus sutirca sp. nov., holotype, no. 5541 (MAIG), habitus: (a) ventral view; (b) dorsal view; (c) left lateral view; (d) frontal view. Scale bar represents 0.2 mm.

Figure 2. X in The first extinct species of Acritus LeConte, 1853 (Histeridae: Abraeinae) from Eocene Baltic amber: a microscopic beetle inclusion studied with X-ray micro-computed tomography

Figure 2. X-ray micro-CT renderings of Acritus sutirca sp. nov., holotype, no. 5541 (MAIG), habitus: (a) dorsal view; (b) left lateral view; (c) ventral view; (d) right lateral view. Scale bar represents 0.2 mm.

Figure 4. X in The first extinct species of Acritus LeConte, 1853 (Histeridae: Abraeinae) from Eocene Baltic amber: a microscopic beetle inclusion studied with X-ray micro-computed tomography

Figure 4. X-ray micro-CT renderings of Acritus sutirca sp. nov., holotype, no. 5541 (MAIG): (a–d) aedeagus in dorsal, ventral view and lateral views; (e) antennae. Scale bar represents 0.1 mm.

Figure 3. X in The first extinct species of Acritus LeConte, 1853 (Histeridae: Abraeinae) from Eocene Baltic amber: a microscopic beetle inclusion studied with X-ray micro-computed tomography

Figure 3. X-ray micro-CT renderings of Acritus sutirca sp. nov., holotype, no. 5541 (MAIG), habitus: (a) frontal view; (b) caudal view. Scale bar represents 0.2 mm. Abbreviations: a1 – antennomere 1 (scape); ey – compound eye; py – pygidium; pp – propygidium.

opencc-by-4.0Nov 2019View details →

X-ray tomography image data of a graphite foam block (KFoam) and tortuosity analysis

X-ray tomography (CT) image data of a graphite foam block (KFoam). The 3D image was generated with an X-ray tomography scan performed by Dr Llion Evans with Manchester X-ray Imaging Facility equipment, which was funded in part by the EPSRC (grants EP/F007906/1, EP/F001452/1 and EP/I02249X/1). The dataset includes: raw radiographs; scan & reconstruction parameter settings file; reconstructed 3D volume. To visualise the 3D volume use software such as ImageJ (https://imagej.net/Fiji/Downloads). The volume image data (NMT_15_229_LLME_DivInterlayer.raw) is in binary format and has the following characteristics: 1586 x 1567 x 1588; 8-bit; little-endian byte order. The second .zip file is a 200 x 200 x 200 subset of this dataset. This was used to perform a tortuosity analysis on the foam. This dataset includes three sets of tiff images; tomographic slices; binarised slices; skeletonised slices. It also includes an excel file with the results of the tortuosity analysis performed with ImageJ. This data was used originally for the following publications (please cite if re-using the data): Ll.M. Evans, L. Margetts, P.D. Lee, C.A.M. Butler, E. Surrey, “Image based in silico characterisation of the effective thermal properties of a graphite foam”, Carbon, Vol. 143, pp. 542-558, 2018. <a href="https://doi.org/10.1016/j.carbon.2018.10.031">https://doi.org/10.1016/j.carbon.2018.10.031</a> Ll.M. Evans, L. Margetts, P.D. Lee, C.A.M. Butler, E. Surrey, “Improving modelling of complex geometries in novel materials using 3D imaging”, Proceedings of NEA International Workshop on Structural Materials for Innovative Nuclear Systems, Manchester, UK, July 2016. <a href="https://www.oecd-nea.org/science/smins4/documents/P1-18_LlME_SMINS4_paper_reviewed.pdf">https://www.oecd-nea.org/science/smins4/documents/P1-18_LlME_SMINS4_paper_reviewed.pdf</a>

opencc-by-4.0Nov 2019View details →

X-ray tomography (CT) image data of tungsten fusion energy heat exchange components

X-ray tomography (CT) image data of tungsten fusion energy heat exchange components. The dataset includes images of four samples: <ul> <li>CCFE_MB_ROI (Culham Centre for Fusion Energy thermal break concept monoblock, region of interest sample)</li> <li>IPP_Wf-Cu (Max-Planck-Institut für Plasmaphysik tungsten fibre / copper matrix coolant pipe)</li> <li>ITER_HHFT_ROI (ITER reference monoblock which has undergone high heat flux testing, region of interest sample)</li> <li>ITER_MB_ROI (ITER reference monoblock, region of interest sample)</li> </ul> This data was used originally for the following publication (please cite if re-using the data) where further details on the data may be obtained: Ll.M. Evans, L. Margetts, P.D. Lee, C.A.M. Butler, E. Surrey, “Image based in silico characterisation of the effective thermal properties of a graphite foam”, Carbon, Vol. 143, pp. 542-558, 2018. <a href="https://doi.org/10.1016/j.carbon.2018.10.031">https://doi.org/10.1016/j.carbon.2018.10.031</a> Each of the sample directories include reconstructed slices in Tiff format. To visualise the 3D volume use software such as ImageJ (https://imagej.net/Fiji/Downloads). CCFE_MB_ROI also includes raw radiographs; scan & reconstruction parameter settings file. A Neutron CT version of this data is available for comparison: <a href="https://doi.org/10.5281/zenodo.3533418">https://doi.org/10.5281/zenodo.3533418</a> Image-based simulation (IBSim) meshes were generated directly from these datasets: <a href="https://doi.org/10.5281/zenodo.3533422">https://doi.org/10.5281/zenodo.3533422</a>

FIGURE 2 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography

FIGURE 2. Reconstructed tomographic images of the specimen (1) and its internal structure in median section (2). The lower and upper jaws are enlarged in (3) and (4), respectively.

FIGURE 5 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography

FIGURE 5. Three-dimensional reconstruction of the upper and lower jaws preserved in the body chamber of the specimen. The reconstructed parts are inside the specimen (1). The jaws are preserved close to each other (2).

FIGURE 1 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography

FIGURE 1. Left lateral (1), dorsal (2) and ventral (3) views of Phyllopachyceras ezoensis with preserved upper and lower jaws in situ within the body chamber. UMUT MM 27831 (modified from Tanabe et al., 2013).

FIGURE 7 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography

FIGURE 7. Result of segmentation of the upper jaw of the specimen, from frontal (1), rear (2), left-lateral (3) views and the transverse section of the area (4) indicated as a square in (3). The three-dimensional reconstruction (5) shows areal distributions of the "chitinous" lamellae and the calcareous covering. The reconstruction of the transverse section (6), which corresponds to (4), shows the architecture of the outer lamella. The abbreviations are indicated in (5).

FIGURE 6 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography

FIGURE 6. Result of segmentation of the lower jaw of the specimen, from lateral view which is restricted to its anterior and posterior portion (1). Three-dimensional reconstruction (2) suggests a wide distribution of calcareous material. The outer calcareous layer on the outer "chitinous" layer is partly taken off in (2). The transverse section of the area indicated as a square in (1) shows that the calcareous covering of the lower jaw also covers the internal surface of the "chitinous" lamella (3). The abbreviation is indicated in (2).

FIGURE 4 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography

FIGURE 4. Linear absorption coefficient (LAC) of the internal portions of the specimen estimated by their mean luminance values in the tomographic images. The numbers (1)-(10) correspond to the materials in Table 1. The dashed lines indicate the known values for the materials (Chantler et al., 2005) that could be expected to be observed in the specimen. Note that glycine is the most dominant amino acid in jaws of Octopus vulgaris (Hunt and Nixon, 1981). The relationship between LAC values and luminance values is based on the assumption that the LAC values for the surrounding air are zero and that the crystals precipitated in the phragmocone are calcite.

FIGURE 3 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography

FIGURE 3. Serial cross-sections of the body chamber portion of the specimen cut from the venter (1) to the dorsum (4), in which sectioned images of the upper jaw are shown. Note that the vertical stripes are due to the separated scanning.

FIGURE 2 in Late Jurassic jaw bones of Halecomorph fish (Actinopterygii: Halecomorphi) studied with X-ray microcomputed tomography

FIGURE 2. Panoramic view of the highest level of exploitation in Owadów-Brzezinki quarry (i.e., unit III and most fossiliferous 'Corbulomima horizon' occurring in the middle of the quarry wall).

FIGURE 4 in Late Jurassic jaw bones of Halecomorph fish (Actinopterygii: Halecomorphi) studied with X-ray microcomputed tomography

FIGURE 4. Maxillary bone of osteichthyan fish Caturus sp. (ZPAL P.16/O-B/2): 1-2. reconstruction of 3-D 'virtual fossils'— the same specimen after digital processing and analysis of tomographic data (scale bars equal 10 mm). 3. vertical sections of Caturus sp. teeth. 4. just after discovery.

FIGURE 1 in Late Jurassic jaw bones of Halecomorph fish (Actinopterygii: Halecomorphi) studied with X-ray microcomputed tomography

FIGURE 1. Map of Poland (1) with the location of the Owadów-Brzezinki Quarry (2B) near Tomaszów Mazowiecki.

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).

opencc-by-4.0Feb 2016View details →

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.