Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
243
datasets available to search
ShareScore release 0.9.0
Dataset results
243 results for “X-ray tomography”
Fig. 21 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 21. Coronal CT images showing variation in the number of ectoturbinals (char. 19). (A) one ectoturbinal is present (char. 19.0), Tarsipes rostratus, C449 (AMNH 119717), scale bar equals 1 mm; (B) two ectoturbinals (char. 19.1), Didelphis virginiana, C464 (TMM M-2517), scale bar equals 5 mm; (C) three ectoturbinals (char. 19.2), Wallabia bicolor, C430 (TMM M-4169), scale bar equals 5 mm; (D) four ectoturbinals (char. 19.3) Potorous tridactylus, C495 (AMNH 65337), scale bar equals 5 mm. Abbreviations: Ecto, ectoturbinal; Endo, endoturbinal; NPM, nasopharyngeal meatus; ONS, ossified nasal septum; SER, sphenethmoid recess.
Fig. 2 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 2. Modified strict consensus tree from Sánchez-Villagra et al. (2007) based on morphological data. Taxa for which I do not have nasal cavity data were pruned from the topology or if possible substituted for closely related species for which I do have nasal cavity data. Wallabia was substituted for Macropus; Sarcophilus was substituted for Dasyuroides; Isoodon was substituted for Perameles. Substitutions within Marsupialia were based on the topologies by Cardillo et al. (2004). For explanation of outgroups used, see caption for figure 1.
Fig. 6 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 6. Coronal CT images showing the packing of endo- and ectoturbinals (char. 14). (A) turbinals are relatively loosely packed (char. 14.0), Caluromys philander, C330 (AMNH 95526); (B) turbinals are complexly branching or convoluted elements that are densely packed creating a tight mazelike pattern, especially around the ossified nasal septum (char. 14.1), Potorous tridactylus, C440 (AMNH 65337). Both scale bars equal 5 mm. Abbreviations: Ecto, ectoturbinal; Endo, endoturbinal; NPM, nasopharyngeal meatus; ONS, ossified nasal septum; PTL, posterior transverse lamina; SER, sphenethmoid recess.
Fig. 20 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 20. Coronal CT images showing the number of turbinal folds on endoturbinal I (char. 15). (A) one (ch. 15.1), Monodelphis domestica, C205 (TMM M-7599); (B) two (char. 15.2), Didelphis virginiana, C464 (TMM M-2517). All scale bars equal 5 mm. Abbreviations: Ecto, ectoturbinal; Endo, endoturbinal; NPM, nasopharyngeal meatus; ONS, ossified nasal septum; PTL, posterior transverse lamina; SER, sphenethmoid recess.
Fig. 19 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 19. Coronal CT images showing pneumaticity of the rostral portion of endoturbinal I (char. 17). (A) rostral portion contains no pneumatic cavities (char. 17.0), Petauroides volans, C370 (AMNH 150055); (B) small pneumatic cavity is present, which encompasses only a portion of the coronal cross section of the element (char. 17.1), Phalanger orientalis, C160 (AMNH 157211); (C) large cavity is present, which encompasses most or the entire coronal cross section of the element (char. 17.2), Didelphis virginiana, C270 (TMM M-2517). All scale bars equal 5 mm. Abbreviations: Endo, endoturbinal; ONS, ossified nasal septum; P1, first upper premolar.
Fig. 4 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 4. Digital rendering of the ethmoid bones (shown in color) inside the semitransparent skull of Didelphis virginiana (TMM M-2517) shown in (A) dorsal, and (B) left lateral views. Scale bar equals 1 cm.
Fig. 1 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 1. Modified topology from Meredith et al. (2009) based on Bayesian analysis of five nuclear genes. Taxa for which I do not have nasal cavity data were pruned from the topology or if possible substituted for closely related species for which I do have nasal cavity data. Didelphis was used as a representative of Didelphinae; Dendrolagus was substituted for Aepyprymnus; Wallabia was substituted for Macropus; Sminthopsis was substituted for Phascolosorex. Substitutions within Marsupialia were based on the topologies by Cardillo et al. (2004). The outgroups were pruned from the topology of Meredith et al. (2009) and instead the following taxa for which I have nasal cavity data were included: Mus, Pteropus, Erinaceus, Ornithorhynchus, and Tachyglossus. The polytomy for the placental mammals reflects the uncertainty in higher level systematics for Placentalia, whereas the monotreme relationships are well established (e.g., Rowe et al., 2008).
Fig. 24 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 24. Coronal CT images showing the presence or absence of prominent lateral expanded bulges within the shaft of the ossified nasal septum (char. 31). (A) bulges present (char. 31.0), Dromiciops gliroides, C136 (FMNH 127463), scale bar equals 1 mm; (B) bulges absent (char. 31.1), Wallabia bicolor, C386 (TMM M-4169), scale bar equals 5 mm. Abbreviations: Ecto, ectoturbinal; Endo, endoturbinal; ONS, ossified nasal septum; SER, sphenethmoid recess.
Fig. 23 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 23. Digital renderings of the cribriform plate showing the presence or absence of a crista galli (char. 34). (A) crista galli is present (char. 34.0), Caluromys philander (AMNH 95526); (B) crista galli is absent (char. 34.1), Dendrolagus lumholtzi (AMNH 65254). Both scale bars equal 1 mm.
Fig. 13 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 13. Coronal CT images showing the morphology of the caudodorsal portion of caudal nasoturbinal (caudal to nasoturbinal division around endoturbinal I; char. 10). (A) caudodorsal portion is unfolded (ch. 10.0), Dromiciops gliroides, C245 (FMNH 127463), scale bar equals 1 mm; (B) caudodorsal portion curls (char. 10.1), Phalanger orientalis, C250 (AMNH 157211), scale bar equals 5 mm. Abbreviations: Ecto, ectoturbinal; Endo, endoturbinal; ONS, ossified nasal septum; SER, sphenethmoid recess.
Fig. 8. Schematic diagram showing a in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 8. Schematic diagram showing a dorsal view of the paries nasi of the chondrocranium of a marsupial. Rostral is to the left. Figure modeled after Smith and Rossie (2006: fig. 8.4). Abbreviations: EC, ectoturbinal; EN, endoturbinal.
Fig. 28 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 28. Coronal CT images showing the complexity of the rostral portion of the maxilloturbinal in marsupials (char. 1). (A) arborlike maxilloturbinal (char. 1.0), Dasyurus hallucatus, C208 (TMM M-6921); (B) simple maxilloturbinal (char. 1.1), Isoodon macrourus, C150 (TMM M-6922); (C) curled lamella (char. 1.1), Phascolarctos cinereus, C129 (TMM M-2946). All scale bars equal 5 mm. Abbreviations: Endo, endoturbinal; ONS, ossified nasal septum.
Fig. 16 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 16. Coronal CT images showing the caudalmost extent of ventral attachment of nasoturbinal (char. 13). (A) attachment is rostral to caudal terminus of maxilloturbinal (char. 13.0), Petauroides volans, C450 (AMNH 150055); (B) attachment is at coronal level of caudal terminus of maxilloturbinal (char. 13.1), Trichosurus vulpecula, C212 (TMM M-849); (C) attachment is caudal to caudal terminus of maxilloturbinal (char. 13.2), Isoodon macrourus, C374 (TMM M-6922). All scale bars equal 5 mm. Abbreviations: Ecto, ectoturbinal; Endo, endoturbinal; ONS, ossified nasal septum; PTL, posterior transverse lamina.
Fig. 12 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 12. Coronal CT images showing the morphology of the caudal nasoturbinal (char. 7). (A) caudal nasoturbinal is unbranched (char. 7.0), Dromiciops gliroides, C230 (FMNH 127463); (B) caudal nasoturbinal has at least one branch (char. 7.1), Caenolestes fuliginosus, C389 (KU 124015). Both scale bars equal 1 mm. Abbreviations: Ecto, ectoturbinal; Endo, endoturbinal; ONS, ossified nasal septum.
Fig. 27 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 27. Coronal CT images showing the morphology of the maxillary recess (char. 26). (A) caudal portion of recess is medially enclosed by posterior transverse lamina (char. 26.0), Dasyurus hallucatus, C330 (TMM M-6921), scale bar equals 5 mm; (B) uncinate process of the caudal nasoturbinal also contributes to the medial wall of the recess (char. 26.1), Monodelphis domestica, C190 (TMM M-7599), scale bar equals 1 mm. Abbreviation: Ecto, ectoturbinal; Endo, endoturbinal; ONS, ossified nasal septum; NPM, nasopharyngeal meatus; PTL, posterior transverse lamina; SER, sphenethmoid recess.
Gel phantom data for dynamic X-ray tomography
<p>The gel phantom was constructed to simulate diffusion of liquids inside plant stems, namely the flow of iodine-based contrast agents used in high resolution tomographic X-ray imaging of plants. In order to test different reconstruction methods, this radiation resistant phantom with similar diffusion properties was constructed.</p> <p>A more detailed documentation can be found on arXiv: <a href="https://arxiv.org/abs/2003.02841">https://arxiv.org/abs/2003.02841</a></p> <p>The phantom consists of a 50 ml Falcon test tube filled with agarose gel. After the agarose solidified, five cavities were made into the gel and filled with 20% sucrose solution to guarantee the diffusion by directing osmosis to the gel body. In addition densely punctured plastic straws were placed in the cavities to simulate cellular passages such as <em>phloem plasmodesmata</em> and to slow down the lateral diffusion.</p> <p>The primary measurements consisted of 17 consecutive time frames, with initial stage of no contrast agent followed<br> by steady increase and diffusion into the gel body over time. Each round of measurements consist of 360 projections with a fanbeam microCT-scanner, but we used only the central plane of the cone beam, resulting in 2D fan beam geometry.</p> <p>Data is given in two different resolutions corresponding to reconstructions of size 256 x 256 or 512 x 512, (<em>GelPhantomData_b4.mat</em> and <em>GelPhantomData_b2.mat</em> respectively). In addition to the primary measurements, a more densely sampled measurements from the first time step and an additional 18th time step are provided in <em>GelPhantom_extra_frames.mat</em>.</p> <p>The measurements are stored in special data structures containing all the necessary metadata. In combination with the MATLAB toolboxes this allows for easy application of forward operators and reconstruction algorithms.</p> <p>This is demonstrated using the included example codes. These require ASTRA Toolbox, Spot Linear Operator Toolbox and HelTomo Toolbox (v1) for MATLAB.</p> <p><strong>NOTE</strong>: Some of the metadata field names are different in HelTomo v2 and higher. Use of the data requires renaming (or adding) two fields in to the parameters:<br> numDetectorsPost = numDetectors;<br> effectivePixelSizePost = effectivePixelSize;<br> <strong>Update: </strong>in v1.2 the data and example codes have been updated to match HelTomo v2.1 convention. For backwards compatibility (with Heltomo 1.0) the old medatadata field names remain.</p> <p>The full cone-beam measurements and corresponding documentation are available in <a href="https://doi.org/10.5281/zenodo.7739984">Zenodo</a>.</p>
Supplementary data to 'The origin and differentiation of CO2-rich primary melts in Ocean Island volcanoes: Integrating 3D X-ray tomography with chemical microanalysis of olivine-hosted melt inclusions from Pico (Azores).'
<p>Supplementary data to:</p><blockquote><p>The origin and differentiation of CO2-rich primary melts in Ocean Island volcanoes: Integrating 3D X-ray tomography with chemical microanalysis of olivine-hosted melt inclusions from Pico (Azores).</p></blockquote>
Data for: Mechanisms of root-reinforcement in soils: an experimental methodology using four-dimensional X-ray computed tomography and digital volume correlation
<p>Collection of data files used in the paper titled: Mechanisms of root-reinforcement in soils: an experimental methodology using four-dimensional X-ray computed tomography and digital volume correlation.</p> <p>Additional dataset which covers the noise study CT scans and digital volume correlation noise studies can be found in DOI: <a href="http://www.doi.org/10.5281/zenodo.3352268">10.5281/zenodo.3361832</a></p> <p><strong>Data contains the following:</strong></p> <ul> <li>X-ray CT data for the interrupted direct shear tests of a soil sample containing a Willow plant. The first file is the specimen scanned unloaded, followed by seven incremental shear load steps to 20 mm shear displacement. Files are 8-bit unsigned and 1800x1800x1600px. Voxel resolution is 0.04642 mm. <ol> <li><strong>20180430_HUTCH_1839_DJB_willow_C_8-bit_1800x1800x1600.raw</strong></li> <li><strong>20180430_HUTCH_1839_DJB_willow_C_Load_A_8-bit_1800x1800x1600.raw</strong></li> <li><strong>20180430_HUTCH_1839_DJB_willow_C_Load_B_8-bit_1800x1800x1600.raw</strong></li> <li><strong>20180430_HUTCH_1839_DJB_willow_C_Load_C_8-bit_1800x1800x1600.raw</strong></li> <li><strong>20180430_HUTCH_1839_DJB_willow_C_Load_D_8-bit_1800x1800x1600.raw</strong></li> <li><strong>20180430_HUTCH_1839_DJB_willow_C_Load_E_8-bit_1800x1800x1600.raw</strong></li> <li><strong>20180430_HUTCH_1839_DJB_willow_C_Load_F_8-bit_1800x1800x1600.raw</strong></li> <li><strong>20180430_HUTCH_1839_DJB_willow_C_Load_G_8-bit_1800x1800x1600.raw</strong></li> </ol> </li> <li>Direct shear vs. displacement data is presented in an Excel spreadsheet: <ul> <li><strong>All_load_data_with_reducing_area.xlsx</strong></li> </ul> </li> <li>Normal and shear strain DVC data which has been averaged and plotted against specimen depth is presented in an Excel spreadsheet: <ul> <li><strong>Average_slice_vs_depth_data_all_samples_all_loads3.xlsx</strong></li> </ul> </li> <li>CT scan metadata giving information to the scan settings, voxel resolution, etc. is contained in a .zip file which consists of .xtekct and .XML files generated from the Nikon CT scanner. <ul> <li><strong>CT_Scan_Metadata.zip</strong></li> </ul> </li> <li>Drawings and Solidworks CAD files of the direct shear test rig are contained within the .zip file. There are a number of parts to the assembly. The file SSSB1003-5.SLDASM contains the complete assembly of the direct shear rig and will help identify the part names. The folder CAD_Drawings contains pdf documents of the part drawings. <ul> <li><strong>Direct_Shear_Drawings_Solidworks_Files.zip</strong></li> </ul> </li> <li>Tabulated DVC data taken at 32x32x32px subset size is contained inside a .zip file. These consist of tab separated .dat files from unloaded (data_1.dat) through incremental load steps Load A, Load B... Load G, (data_2.dat, data_3.dat... data_8.dat). The structure of the .dat file contains columns of data with each column number corresponding to the following: (1) x, (2) y (3) z, (4) vx, (5) vy, (6) vz, (7) exx, (8) eyy, (9) ezz, (10) exy, (11) exz, (12) eyz, (13) volumetric strain, (14) is valid. Columns 1-3 are subset positions in mm, 4-6 are displacements in mm, 7-9 are normal strains, 10-12 are shear strains, 13 is volumetric strain and 14 is a binary value indicating if the subset is valid. <ul> <li><strong>DVC_Load_Data_Willow_C.zip</strong></li> </ul> </li> <li>Tabulated DVC data applied to the load step CT data at 32, 48, 64, 96, 128 pixels is presented in the .zip files containing .dat tab separated files. The structure of the .dat files is described in the previous bullet point. These files were used to construct the noise study applied to incrementally loaded CT data by sampling regions away from the shear zone where the strain signals are close to zero. <ul> <li><strong>DVC_Noise_Study_Data_Load_Steps_Willow_C.zip</strong></li> </ul> </li> <li>Processed noise study data which compares the effects of DVC subset size is presented in the .xlsx file. This file contains both the controlled noise experiment data (stationary, magnification and rigid body motion) and noise study data applied to incrementally loaded data using sampled regions away from the shear zone where the strain signals are close to zero. <ul> <li><strong>Willow_C_Processed_Noise_study2.xlsx</strong></li> </ul> </li> <li>Tabulated data which compares the local x displacement vs depth profile from DVC and direct measurement of root position is contained in the following Excel spreadsheet file: <ul> <li><strong>X_Displacement_Root_and_DVC_Comparison_Willow C.xlsx</strong></li> </ul> </li> </ul>
Image Dataset for 'Digitally deconstructing leaves in 3D using X-ray microcomputed tomography and machine learning'
<p>Dataset used in the manuscript 'Digitally Deconstructing Leaves in 3D Using X-ray microcomputed Tomography and Machine Learning'. Please cite the paper presenting this dataset:</p> <p><strong>Citation:</strong> Théroux-Rancourt, G., M. R. Jenkins, C. R. Brodersen, A. McElrone, E. J. Forrestel, and J. M. Earles. 2020. Digitally deconstructing leaves in 3D using X-ray microcomputed tomography<strong> </strong>and machine learning. <em>Applications in Plant Sciences</em> 8(7): .</p> <p> </p> <p><strong>Description of the dataset</strong></p> <p>A 'Cabernet Sauvignon' grapevine (<em>Vitis vinifera</em> L.) leaf from a plant of the BOKU experimental vineyard in Tulln, Austria, was scanned using microCT at the Swiss Light Source. The original reconstructions of the scans are using the gridrec (<a href="https://zenodo.org/api/files/bbca544a-15d0-40f3-8cc9-a3ee3c08fd7e/Gridrec_reconstruction_downsized.zip?versionId=28d98982-f69d-4eac-9dfa-efcc89c6823c">Gridrec_reconstruction_downsized.zip</a>) and the paganin, or phase-contrast, algortithm (<a href="https://zenodo.org/api/files/bbca544a-15d0-40f3-8cc9-a3ee3c08fd7e/Phase_contrast_reconstruction_downsized.zip?versionId=bef3260d-2865-4c9b-b5e1-e692edefb691">Phase_contrast_reconstruction_downsized.zip</a>). To facilitate automated segmentation, the size of the image in the <em>x </em>and <em>y</em> dimensions have been halved, so that the size of the pixels is 0.325 µm in those dimensions, but 0.1625 µm in the <em>z</em> (slices) dimension.</p> <p>A binary image segmenting the leaf cells and the airspace for each gridrec and phase-contrast stacks are created, and both are combined together (<a href="https://zenodo.org/api/files/bbca544a-15d0-40f3-8cc9-a3ee3c08fd7e/Binary_stack_for_local_thickness.zip?versionId=165e3938-b490-4e56-9c8e-a2084cb39d49">Binary_stack_for_local_thickness.zip</a>), a map of the local thickness is created (<a href="https://zenodo.org/api/files/bbca544a-15d0-40f3-8cc9-a3ee3c08fd7e/Local_thickness_map.zip?versionId=ce0a7dc7-5e3f-44a4-8881-cf84b6efd87c">Local_thickness_map.zip</a>). This map gives information on the largest diameter of the pixels labeled as cells in the binary stack.</p> <p>Hand-labeled slices or ground truths were drawn on the following slices: 80, 140, 200, 260, 340, 400, 440, 540, 620, 740, 800, 860, 940, 1060, 1140, 1240, 1300, 1400, 1480, 1540, 1600, 1690, 1740, 1840 (<a href="https://zenodo.org/api/files/bbca544a-15d0-40f3-8cc9-a3ee3c08fd7e/Hand_labelled_slices.tif?versionId=a21a13ac-fa47-4ef8-a903-ecc433787184">Hand_labelled_slices.tif</a>).</p> <p>Using the hand-labeled slices and the different images, a random-forest model was trained, which allowed to automatically segment the remaining slices of the stack (<a href="https://zenodo.org/api/files/bbca544a-15d0-40f3-8cc9-a3ee3c08fd7e/Fullstack_Prediction_Example-6_training_slices-6_testing_slices.zip?versionId=02b69e65-da85-492e-9b72-9b2b3ccd085f">Fullstack_Prediction_Example-6_training_slices-6...</a>).</p> <p>The source code for the segmentation program is available <a href="https://github.com/plant-microct-tools/leaf-traits-microct/tree/master">here</a>, and the source code for the testing used in the paper is available <a href="https://github.com/plant-microct-tools/leaf-traits-microct/tree/nb-slices-eval">here</a>.</p>
Geometric calibration of a double-line X-ray cone-beam tomography system
<p>This dataset correspond to the raw data and measurements presented in the article "Geometric calibration of a double-line X-ray cone-beam tomography system". In this study, an existing single-line calibration method is extended to the case of a double-line X-ray tomograph, based only on the geometrical relation between the different components, and using a simplified calibration phantom. The methodology is tested on the new double tomograph system at INSA Lyon. Walnuts are used as testing phantoms due to their natural irregularity and outstanding internal texture under X-rays.</p><p>Two scanning scenarios are selected to represent the wide range of possible geometries that the system can resolve. The first test, referred to as NXGP04, corresponds to an assembly of walnuts inside a container, scanned at a voxel size of 111 μm, and a geometric magnification (i.e., the ratio between SDD and SOD) of 2.7. The second test, referred to as NXGP05, constitutes a scan of a single walnut using a voxel size of 28 μm and a geometric magnification of 10.7. For a given test, all the geometric parameters (i.e., SOD and SDD), as well as the scanning parameters (e.g., voltage and exposure time) are set equally for both lines. </p><p>Calibration phantoms are used to measure the geometry of the system for each test. They consist of a set of 7 metallic spheres attached to a foam board arranged along a line. For the test NXGP04, the spheres have 2.5 mm in diameter and are placed using a spacing of 20 mm, while for the test NXGP05, the spheres have 0.8 mm in diameter and spacing of 8.75 mm. In both cases, the size of the spheres in the detectors is such that more than 700 pixels are used to determine their centre, which increases the sensitivity of the calculation. </p>
ScienceDex guides
Understand access before you commit
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.