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25 results for “digital tomography”
Data set for "Axonal and dendritic morphology of excitatory neurons in layer 2/3 mouse barrel cortex imaged through whole-brain two-photon tomography and registered to a digital brain atlas"
<p>Data set for: Liu Y, Foustoukos G, Crochet S and Petersen CCH (2022) Axonal and dendritic morphology of excitatory neurons in layer 2/3 mouse barrel cortex imaged through whole-brain two-photon tomography and registered to a digital brain atlas. Front Neuroanat 15: 791015. https://doi.org/10.3389/fnana.2021.791015</p> <p>There are 2 files in this upload:</p> <p>1. The file named "<strong>2022_Liu_FrontNeuroanat.pdf</strong>" is the Open Access pdf of the online publication in Frontiers in Neuroanatomy.</p> <p>2. The file named "<strong>Liu_data_code.zip</strong>" (~1 GB) is a zipped version of a folder ‘<em>Liu_data_code</em>’, which contains the data analyzed in the study along with the Python codes used to generate the published figures. The original high resolution image stacks obtained through whole-brain two-photon serial tomography are unfortunately too large for Zenodo, and only highly-downsampled data are included in this upload, which were used for registration with the Allen CCFv3. Instructions on how to view and analyse the anatomical data are provided in the 'README.docx' file, which you will find upon unzipping the folder.</p> <p> </p>
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>
Comparison of Full-Field Digital Mammography With Digital Breast Tomography for Screening Call-Back Rates
ClinicalTrials.gov study NCT01236781. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Noise study data for: Mechanisms of root-reinforcement in soils: an experimental methodology using four-dimensional X-ray computed tomography and digital volume correlation
<p>This dataset contains noise study data used in the paper: Mechanisms of root-reinforcement in soils: an experimental methodology using four-dimensional X-ray computed tomography and digital volume correlation. These include raw CT scans and processed digital volume correlation data.</p> <p>This dataset is part of another dataset which covers other aspects of the paper DOI: <a href="http://www.doi.org/10.5281/zenodo.3352268">10.5281/zenodo.3352268</a></p> <p>The structure of the dataset is as follows:</p> <ul> <li>Noise study CT raw volumes are contained in a zip file. There are four raw files corresponding to the four noise study steps. These files are 8-bit unsigned, dimensions are 1800 x 1800 x 1400 pixels. A txt file giving more details to the data is included. <ul> <li><strong>CT_Raw_data_Noise_Scans.zip</strong></li> </ul> </li> <li>Metadata files generated for each scan given details of scan parameters are found in the zip file: <ul> <li><strong>CT_Scan_Metadata.zip</strong></li> </ul> </li> <li>Tabulated digital volume data for the noise study scans are contained in the zip file. Tabulated data for each subset size is included in subfolders. A .txt file explains the structure of the tab separated .dat files, i.e. what each column of data represents, and what CT scan each of the four .dat files relate to. <ul> <li><strong>DVC_Noise_Study_Data.zip</strong></li> </ul> </li> </ul> <p> </p> <p> </p>
Comparison of planar digital radiography and helical standing computed tomography for assessment of condylar stress fracture risk in Thoroughbred racehorses
<p class="MsoNormal"><strong>Background</strong>: Catastrophic injury has a low incidence but leads to the death of many Thoroughbred racehorses.</p> <p class="MsoNormal"><strong>Objectives</strong>: To determine sensitivity, specificity, and reliability for condylar stress fracture risk assessment from fetlock digital radiographs (DR) and standing computed tomography (sCT).</p> <p class="MsoNormal"><strong>Study design</strong>: Controlled <em>ex vivo</em> experiment.</p> <p class="MsoNormal"><strong>Methods</strong>: A blinded set of thoracic limb fetlock DR and sCT images were prepared from 31 Thoroughbreds. Four observers evaluated the condyles and parasagittal grooves (PSG) of the third metacarpal bone for the extent of dense bone and lucency/fissure and assigned a risk assessment grade for condylar stress fracture. Sensitivity and specificity for detection of subchondral structural changes in the condyles and PSG and for risk assessment for condylar stress fracture were determined by comparison with a reference. Agreement between observers and the reference assessment and reliability between observers were determined. Intra-observer repeatability was also assessed.</p> <p class="MsoNormal"><strong>Results</strong>: Sensitivity for detection of structural change was lower than specificity for both imaging methods and all observers. For horses with normal risk, observer assessment often agreed with the reference. Sensitivity for risk assessment was lower than specificity for all observers. For horses with a high risk of injury, observers generally underestimated risk. Diagnostic sensitivity of risk assessment was improved with sCT imaging, particularly for horses with elevated risk of injury. Assessment repeatability and reliability was better with sCT than DR.</p> <p class="MsoNormal"><strong>Main limitations</strong>: The <em>ex vivo</em> study design influenced DR image sets.</p> <p class="MsoNormal"><strong>Conclusions</strong>: Risk assessment through screening with diagnostic imaging is a promising approach to improve injury prevention in racing Thoroughbreds. Knowledge of sensitivity and specificity of fetlock lesion detection provides the critical guidance needed to improve screening programs for racehorses. We found improved detection of MC3 subchondral structural change and risk assessment for condylar stress fracture with sCT <em>ex vivo</em>.</p>
Figure 13 in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 13. Rooted maximum likelihood tree of the Orchomene s.l. complex COI. Bootstrap support is shown for each branch. Hirondellea gigas was used as the outgroup. Ŋe position of Orchomenella rinamontiae is shown in yellow.
Figure 11 in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 11. Orchomenella rinamontiae. Holotype, ♀, 24.4 mm. Less uropods (U1, U2, and U3) and telson (T) in dorsal view. Scale bars: 0.5 mm.
Figure 12 in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 12. Unrooted non-redundant maximum likelihood tree of the Lysianassoidea COI. Leaves represent individual specimens, coloured by genus where this information was available in the NCBI database. Our samples of Orchomenella rinamontiae, from both RNA sequencing and DNA sequencing, are coloured in red. Ŋe area of the tree illustrated in Figure 13 is enclosed by a grey doưed line. A complete list of sequences in each genus group can be found in the Supporting Information (Table S1).
Figure 9. Synchrotron radiation X in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 9. Synchrotron radiation X-ray phase-contrast micro-tomography (A, B) and scanning electron microscopy (C–F) of gnathopods of Orchomenella rinamontiae. Paratypes, ♂♂, 11.3 mm (A, B) and 11.3 and 15.4 mm (C–F). A, lateral view of right gnathopod 2. B, medial view of right gnathopod 2. C, lateral view of less gnathopod 1. D, medial view of right gnathopod 1. E, lateral view of less gnathopod 2. F, medial view of right gnathopod 2. Abbreviations: a, gnathopod 1 lateral spine; b, gnathopod 1 medial spine; c, gnathopod 2 tip of dactyl. Scale bars: 200 µm.
Figure 10 in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 10. Orchomenella rinamontiae. Holotype, ♀, 24.4 mm. Medial view of less gnathopod 2 (Gn2). Scale bars: 1 mm.
Figure 8 in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 8. Orchomenella rinamontiae. Holotype, ♀, 24.4 mm. Right maxilliped (Mxpd) and less inner plate (L inner pl). Scale bars: 0.1 mm for L inner pl; 0.5 mm for Mxpd.
Figure 7 in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 7. Scanning electron microscopy of maxillipeds of Orchomenella rinamontiae. Paratypes, ♂♂, 15.4 and 16.8 mm. A, anterior/dorsal view. B, less dorsal view. C, dorsal view of outer and inner plates. D, higher magnification of the tip of the right outer plate. E, dorsal view of right palp. Scale bars: 200 µm in A–C; 20 µm in D; 100 µm in E.
Figure 1. Synchrotron radiation X in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 1. Synchrotron radiation X-ray phase-contrast micro-tomography of Orchomenella rinamontiae. Paratype, ♂, 11.3 mm. Volume renderings of lateral less view (A) and ventral view (B). Abbreviations: A1, antenna 1; A2, antenna 2; Gn1, gnathopod 1; Gn2, gnathopod 2. Scale bar: 4.0 mm.
Figure 5 in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 5. Scanning electron microscopy of mandibles of Orchomenella rinamontiae. Paratypes, ♂♂, 15.4 and 16.8 mm. A, B, less palp in median view (A) and lateral view (B). C, D, less mandible in median view (C) and dorsal view (D). Abbreviations: i, incisor; l, lacinia mobilis; m, molar process. Scale bars: 200 µm in A, B; 50 µm in C; 40 µm in D.
Figure 4. Synchrotron radiation X in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 4. Synchrotron radiation X-ray phase-contrast micro-tomography of Orchomenella rinamontiae. Paratype, ♂, 11.3 mm. Volume renderings of the mouth in ventral view (A), higher magnification of the right mouthparts in ventral view (B), right mouthparts in median view (C), and mouth in dorsal view with the observation point inside the animal (D). Abbreviations: a, outer plate maxilliped; b, inner plate maxilliped; c, outer plate maxilla 2; d, inner plate maxilla 2; e, palp maxilla 1; f, outer plate maxilla 1; g, inner plate maxilla 1. Scale bars: 200 µm.
Figure 6 in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 6. Scanning electron microscopy of maxillae of Orchomenella rinamontiae. Paratypes, ♂♂, 15.4 and 16.8 mm. A, right maxilla 2 in median view. B, right maxilla 1 in median view. C, less maxilla 1 in median view. D, right maxilla 1 inner plate in median view. E, F, outer plates of right maxilla 1 (E) and less maxilla 1 (F) in median view. G, tip of maxillular palp. Scale bars: 100 µm in A–C; 40 µm in D–G.
Figure 3 in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 3. Scanning electron microscopy of antenna 1 of Orchomenella rinamontiae. Paratype, ♂, 11.3 mm. Calceoli (white arrows) are present on each flagellar article. A–C, neighbouring calceoli are orientated the same on the proximal part of the flagellum (A, B) and rotated by ~90° on the distal part (C). D, a higher magnification of a lateral view of a calceolus. Abbreviation: a, callynophore. Scale bars: 100 µm in A; 20 µm in B, C; 10 µm in D.
Figure 2 in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 2. Scanning electron microscopy of antenna 1 of Orchomenella rinamontiae. Paratype, ♂, 11.3 mm. Scale bar: 200 µm.
Comparison of planar digital radiography and helical standing computed tomography for assessment of condylar stress fracture risk in Thoroughbred racehorses
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