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18 results for “µCT”
Supplementary data for "Armored with skin and bone: A combined histological and µCT study of the exceptional integument of the Antsingy leaf chameleon Brookesia perarmata (Angel, 1933)"
<p>This project contains the supplementary µCT-scans of the whole body and a lateral flank integumentary armor of <em>Brookesia perarmata</em> (Angel, 1933) (Squamata: Iguania: Chamaeleonidae) belonging to the following publication:</p> <p>Schucht P, Rühr PT, Geier B, Glaw F & M LAmbertz (<strong>2020</strong>): Armored with skin and bone: A combined histological and µCT study of the exceptional integument of the Antsingy leaf chameleon <em>Brookesia perarmata</em> (Angel, 1933). <em>Journal of Morphology</em>. doi: <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/jmor.21135">10.1002/jmor.21135</a>.</p> <p> </p> <p><strong>Whole body scan:</strong></p> <ul> <li>specimen: ZSM 17/2006, Zoologische Staatssammlung München</li> <li>machine: phoenix nanotom m (GE Measurement & Control)</li> <li>scan settings: <ul> <li>tube voltage = 110 kV</li> <li>ube current = 70 μA</li> <li>target = tungsten</li> <li>no filter</li> <li>total sample rotation = 360°</li> <li>angular step size = 0.24°</li> <li>exposure time = 750 ms</li> <li>binning = 1</li> <li>averaging = 4</li> <li>voxel size = 37.8 μm</li> </ul> </li> <li>filename: Schucht_B_perarmata_whole.tif</li> </ul> <p> </p> <p><strong>Lateral flank integumentary armor scan:</strong></p> <ul> <li>specimen: ZSM 862/2000, Zoologische Staatssammlung München</li> <li>machine: Skyscan 1272 device (Bruker microCT)</li> <li>scan settings: <ul> <li>tube voltage = 70 kV</li> <li>ube current = 142 μA</li> <li>target = tungsten</li> <li>filter = Al 0.5 mm</li> <li>total sample rotation = 180°</li> <li>angular step size = 0.19°</li> <li>exposure time = 1925 ms</li> <li>binning = 2x2</li> <li>averaging = 8</li> <li>random movement = 15</li> <li>voxel size = 4.4 μm</li> </ul> </li> <li>filename: Schucht_B_perarmata_osteoderm.tif</li> </ul>
SkyScan 1172 µCT dataset of grains
<p>This is a micro-CT dataset obtained from SkyScan 1172. A collection of grains were imaged with a total of 996 projections. Metadata needed for reconstruction are included in jyvat.log. The projections are in TIFF-format (16-bit unsigned integers, single channel). This data can also be used as an example data with the OMEGA software.</p> <p>Flat field correction has been most likely applied to the projections, but it is unknown if other corrections has been applied. No flat value is included.</p>
Cryptolacruma nidis (Isopoda: Epicaridea), Kachin amber, PED 0226, µCT scan
<p>Two fossil specimens preserved in Kachin amber (Myanmar, mid-Cretateous), described as <em>Cryptolacruma nidis </em>Schädel, Hörnig, Hyžný & Haug 2021 (https://doi.org/10.1007/s12542-021-00564-9), holotype and paratype, PED 0226, µCT data, 10x objective, 40 kV, 8 W, 4 s exposure time. TIF format, system based calculated pixel size = 1.5 µm.</p>
Nerocila acuminata head µCT scan
<p><em>Nerocila acuminata</em> Leach, 1818, ovigerous female (20 mm), Cross Bay, Rovinji, Croatia (45°7.06′N 13°3.99′E), attached to the vertical fin of a representative of Mugilidae Cuvier, 1829, Roland Melzer 2014 (ZSMA20159001).</p> <p>X-ray µCT scan, performed using a Phoenix (GE Sensing & Inspection Technologies GmbH) Nanotom M scanner, 90 kV, 110 µA, 54 min scan time, 2.3 µm<sup>3</sup> voxel size.</p>
Simultaneous three-dimensional vascular and tubular imaging of whole mouse kidneys with X-ray µCT
<p>µCT dataset of a mouse kidney injected with contrast agent XlinCA and scanned with 3.3 µm voxel size. Detailed sample preparation and image acquisition protocols are published as <a href="https://doi.org/10.1017/S1431927620001725">"Simultaneous three-dimensional vascular and tubular imaging of whole mouse kidneys with X-ray µCT"</a> in <em>Microscopy and Microanalysis</em>.</p> <p>Segmentations of the vascular and tubular lumina along with the renal tissue are provided as masks. The three different segmented features were combined into a single dataset and encoded as different gray values:</p> <p>0: Background<br> 51: Tubules<br> 204: Tissue<br> 255: Blood vessels</p> <p>The Supplemental Video features a computer graphics visualization of the segmented masks. Blood vessel lumina are rendered in red, tissue in transparent blue and tubular lumina in yellow.</p>
Euphrosine foliosa µCT-scan
<p>Image sequence of a reconstructed µCT-scan of <em>Euphrosine foliosa</em> AUDOUIN & MILNE EDWARDS 1833 performed with the following settings</p> <p> </p> <p>[System]<br> Scanner=SkyScan1272<br> Instrument S/N=15H09112<br> Software Version=1.1.10<br> Source Type=HAMAMATSU_L11871_20<br> Camera Type=XIMEA xiRAY16<br> Camera Pixel Size (um)=7.4<br> Camera X/Y Ratio=1.0058<br> <br> Number Of Files= 482<br> Number Of Rows= 1092<br> Number Of Columns= 1632<br> Partial Width=OFF<br> Image crop origin X=0<br> Image crop origin Y=0<br> Camera binning=3x3<br> Image Rotation=0.01800<br> Optical Axis (line)= 593<br> Camera to Source (mm)=174.64085<br> Object to Source (mm)=62.93450<br> Source Voltage (kV)= 60<br> Source Current (µA)= 166<br> Image Pixel Size (µm)=8.000109<br> Scaled Image Pixel Size (µm)=8.000109<br> Image Format=TIFF<br> Depth (bits)=16<br> Reference Intensity=57000<br> Exposure (ms)=741<br> Rotation Step (deg)=0.400<br> Use 360 Rotation=NO<br> Scanning position=16.028 mm<br> Frame Averaging=ON (6)<br> Random Movement=OFF (15)<br> Flat Field Correction=ON<br> FF updating interval=161<br> Geometrical Correction=ON<br> Filter=Al 0.25mm<br> Gantry direction=CC<br> Rotation Direction=CC<br> Type of Detector Motion=STEP AND SHOOT<br> Scanning Trajectory=ROUND<br> Number Of Horizontal Offset Positions=1<br> Number of connected scans=3<br> Current scan number=1<br> Number of lines to be reconstructed=732<br> Study Date and Time=28 Jun 2019 12h:28m:47s<br> Scan duration=0h:44m:47s<br> Maximum vertical TS=5.0<br> [Reconstruction]<br> Reconstruction Program=NRecon<br> Program Version=Version: 1.7.1.0<br> Reconstruction engine=InstaRecon<br> Engine version=Version: 2.0.3.7<br> Reconstruction from batch=No<br> Postalignment=7.00<br> Connected Reconstruction (parts)=3<br> Sub-scan post alignment [0]=8.000000<br> Sub-scan post alignment [1]=7.000000<br> Sub-scan post alignment [2]=7.000000<br> Sub-scan scan length [0]=731<br> Sub-scan scan length [1]=731<br> Sub-scan scan length [2]=732<br> Used extra shift in X per scan(micron)= 0.000 -1.262 4.411 <br> Used extra shift in Y per scan(micron)= 0.000 -9.915 -43.932 <br> First Section=175<br> Last Section=2340<br> Reconstruction duration per slice (seconds)=0.110048<br> Total reconstruction time (1463 slices) in seconds=161.000000<br> Section to Section Step=1<br> Sections Count=2166<br> Result File Type=TIF<br> Result File Header Length (bytes)=12<br> Result Image Width (pixels)=840<br> Result Image Height (pixels)=656<br> Pixel Size (um)=8.00011<br> Reconstruction Angular Range (deg)=192.80<br> Use 180+=OFF<br> Angular Step (deg)=0.4000<br> Smoothing=1<br> Smoothing kernel=2 (Gaussian)<br> Ring Artifact Correction=5<br> Draw Scales=OFF<br> Object Bigger than FOV=OFF<br> Reconstruction from ROI=ON<br> ROI Top (pixels)=1182<br> ROI Bottom (pixels)=523<br> ROI Left (pixels)=420<br> ROI Right (pixels)=1263<br> ROI reference length=1632<br> Filter cutoff relative to Nyquist frequency=100<br> Filter type=0<br> Filter type description=Hamming (Alpha=0.54)<br> Undersampling factor=1<br> Threshold for defect pixel mask (%)=0<br> Beam Hardening Correction (%)=40<br> CS Static Rotation (deg)=5.96<br> Minimum for CS to Image Conversion=0.004763<br> Maximum for CS to Image Conversion=0.219915<br> HU Calibration=OFF<br> BMP LUT=0<br> Cone-beam Angle Horiz.(deg)=11.844029<br> Cone-beam Angle Vert.(deg)=7.940657<br> Automatic matching in Z=50<br> Automatic matching in X/Y=50<br> Automatic matching in rotation=0.000000<br> Automatic fusion=1<br> <br> </p>
Chaetopterus norvegicus, µCT
<p>Chaetopterus norvegicus, µCT data-set, 6µm</p> <p>SkyScan, 70 KV</p> <p> </p>
Two fossil isopods from the Middle Jurassic of Bielefeld ES/jb-30755 and ES/jb-30756 µCT scan
<p>Two fossil specimens belonging to the group Isopoda, Middle Jurassic, Bajocian, <em>Parkinsonia parkinsoni</em> Zone, quarry "Bethel 1", Bielefeld, Germany, deposited at the Natural History Museum Bielefeld, accession numbers ES/jb-30755 and ES/jb-30756.</p> <p>X-ray µCT scan, performed using a Phoenix (GE Sensing & Inspection Technologies GmbH) Nanotom M scanner, 120 kV, 100 µA, 18.4464 µm<sup>3</sup> voxel size.</p>
Fossil isopod from the Lower Jurassic of Kircheim unter Teck GPIT-PV-76948 µCT scan
<p>One fossil specimen of the group Isopoda, described as <em>Palaega suevica</em> Reiff, 1936, head and anterior-most trunk region, Lower Jurassic, Pliensbachian, Amaltheenton Formation, Kirchheim unter Teck, Germany, deposited at the collection of the University of Tübingen, accession number GPIT-PV-76948.</p> <p>X-ray µCT scan, performed using a Phoenix (GE Sensing & Inspection Technologies GmbH) Nanotom M scanner, 120 kV, 100 µA, 4.55246 µm<sup>3</sup> voxel size.</p>
Fossil isopod from the Middle Jurassic of Bielefeld ES/jb-8744 µCT scan
<p>One fossil specimen belonging to the group Isopoda, Middle Jurassic, Bajocian, <em>Parkinsonia parkinsoni</em> Zone, quarry "Bethel 1", Bielefeld, Germany, deposited at the Natural History Museum Bielefeld, accession number ES/jb-8744.</p> <p>X-ray µCT scan, performed using a Phoenix (GE Sensing & Inspection Technologies GmbH) Nanotom M scanner, 120 kV, 100 µA, 13.86661 µm<sup>3</sup> voxel size.</p>
Correlative study of liquid in human bone by 3D neutron microscopy and lab-based X-ray µCT
<p>X-ray (xray_data.tiff) and neutron microscopy (neutron_data.tiff) of the same piece of human cortical bone.</p> <p>Neutron data were collected at the neutron microscope at SINQ, PSI, Switzerland while the x-ray data were collected in house at an VERSA 620 X-ray microscope. </p> <p>The voxel size is in both case 2.7 µm</p>
Magelona mirabilis µCT scan
<p>µCT scan of a specimen of <em>Magelona mirabilis</em> stained with PTA for one week. Scan and reconstruction were obtained with the following settings:</p> <p>[System]<br> Scanner=SkyScan1272<br> Instrument S/N=15H09112<br> Software Version=1.1.10<br> Source Type=HAMAMATSU_L11871_20<br> Camera Type=XIMEA xiRAY16<br> Camera Pixel Size (µm)=7.4<br> Camera X/Y Ratio=1.0058<br> <br> [Acquisition]<br> Filename Index Length=8<br> Number Of Files= 940<br> Number Of Rows= 1640<br> Number Of Columns= 2452<br> Partial Width=OFF<br> Image crop origin X=0<br> Image crop origin Y=0<br> Camera binning=2x2<br> Image Rotation=0.00400<br> Optical Axis (line)= 932<br> Camera to Source (mm)=274.64085<br> Object to Source (mm)=55.67001<br> Source Voltage (kV)= 60<br> Source Current (µA)= 166<br> Image Pixel Size (µm)=2.999977<br> Scaled Image Pixel Size (µm)=2.999977<br> Image Format=TIFF<br> Depth (bits)=16<br> Reference Intensity=57000<br> Exposure (ms)=2832<br> Rotation Step (deg)=0.200<br> Use 360 Rotation=NO<br> Scanning position=2.271 mm<br> Frame Averaging=ON (4)<br> Random Movement=OFF (8)<br> Flat Field Correction=ON<br> FF updating interval=55<br> Geometrical Correction=ON<br> Filter=Al 0.25mm<br> Gantry direction=CC<br> Rotation Direction=CC<br> Type of Detector Motion=STEP AND SHOOT<br> Scanning Trajectory=ROUND<br> Number Of Horizontal Offset Positions=1<br> Number of connected scans=3<br> Current scan number=1<br> Number of lines to be reconstructed=1093<br> Scan duration=3h:17m:30s<br> Maximum vertical TS=5.0</p> <p><br> [Reconstruction]<br> Reconstruction Program=NRecon<br> Program Version=Version: 1.7.1.0<br> Reconstruction engine=InstaRecon<br> Engine version=Version: 2.0.3.7<br> Reconstruction from batch=No<br> Postalignment=9.50<br> Connected Reconstruction (parts)=3<br> Sub-scan post alignment [0]=8.500000<br> Sub-scan post alignment [1]=9.000000<br> Sub-scan post alignment [2]=9.500000<br> Sub-scan scan length [0]=1091<br> Sub-scan scan length [1]=1093<br> Sub-scan scan length [2]=1093<br> Used extra shift in X per scan(micron)= 0.000 -1.327 0.089 <br> Used extra shift in Y per scan(micron)= 0.000 -13.707 -21.439 <br> Time and Date=Jul 14, 2021 12:03:18<br> First Section=315<br> Last Section=3430<br> Reconstruction duration per slice (seconds)=0.294737<br> Total reconstruction time (2185 slices) in seconds=644.000000<br> Section to Section Step=1<br> Sections Count=3116<br> Result File Type=TIF<br> Result File Header Length (bytes)=12<br> Result Image Width (pixels)=1960<br> Result Image Height (pixels)=1960<br> Pixel Size (µm)=2.99998<br> Reconstruction Angular Range (deg)=188.00<br> Use 180+=OFF<br> Angular Step (deg)=0.2000<br> Smoothing=0<br> Ring Artifact Correction=8<br> Draw Scales=OFF<br> Object Bigger than FOV=OFF<br> Reconstruction from ROI=ON<br> ROI Top (pixels)=2115<br> ROI Bottom (pixels)=153<br> ROI Left (pixels)=194<br> ROI Right (pixels)=2156<br> ROI reference length=2452<br> Filter cutoff relative to Nyquist frequency=100<br> Filter type=0<br> Filter type description=Hamming (Alpha=0.54)<br> Undersampling factor=1<br> Threshold for defect pixel mask (%)=0<br> Beam Hardening Correction (%)=0<br> CS Static Rotation (deg)=0.00<br> Minimum for CS to Image Conversion=-0.039105<br> Maximum for CS to Image Conversion=0.529521<br> HU Calibration=OFF<br> BMP LUT=0<br> Cone-beam Angle Horiz.(deg)=7.559778<br> Cone-beam Angle Vert.(deg)=5.060351<br> Automatic matching in Z=50<br> Automatic matching in X/Y=50<br> Automatic matching in rotation=0.000000<br> Automatic fusion=1<br> </p> <p>Data size has been reduced by conversion from 16-bit to 8-bit and decreasing the scale of the images.</p>
Sternaspis scutata µCT scan
<p>µCT scan of a specimen of <em>Sternaspis scutata</em> stained with PTA for one week. Scan and reconstruction were obtained with the following settings:</p> <p>[System]<br> Scanner=SkyScan1272<br> Instrument S/N=15H09112<br> Software Version=1.1.10<br> Source Type=HAMAMATSU_L11871_20<br> Camera Type=XIMEA xiRAY16<br> Camera Pixel Size (µm)=7.4<br> Camera X/Y Ratio=1.0058</p> <p>[Acquisition]<br> Number Of Files= 961<br> Number Of Rows= 1640<br> Number Of Columns= 2452<br> Partial Width=OFF<br> Image crop origin X=0<br> Image crop origin Y=0<br> Camera binning=2x2<br> Image Rotation=-0.00100<br> Optical Axis (line)= 890<br> Camera to Source (mm)=174.64085<br> Object to Source (mm)=82.59950<br> Source Voltage (kV)= 70<br> Source Current (µA)= 142<br> Image Pixel Size (µm)=6.999924<br> Scaled Image Pixel Size (µm)=6.999924<br> Image Format=TIFF<br> Depth (bits)=16<br> Reference Intensity=57000<br> Exposure (ms)=1238<br> Rotation Step (deg)=0.200<br> Use 360 Rotation=NO<br> Scanning position=11.719 mm<br> Frame Averaging=ON (4)<br> Random Movement=OFF (15)<br> Flat Field Correction=ON<br> FF updating interval=120<br> Geometrical Correction=ON<br> Filter=Al 0.5mm<br> Gantry direction=CC<br> Rotation Direction=CC<br> Type of Detector Motion=STEP AND SHOOT<br> Scanning Trajectory=ROUND<br> Number Of Horizontal Offset Positions=1<br> Number of connected scans=3<br> Current scan number=1<br> Number of lines to be reconstructed=1036<br> Scan duration=1h:40m:36s<br> Maximum vertical TS=5.0</p> <p>[Reconstruction]<br> Reconstruction Program=NRecon<br> Program Version=Version: 1.7.1.0<br> Reconstruction engine=InstaRecon<br> Engine version=Version: 2.0.3.7<br> Reconstruction from batch=Yes<br> Postalignment=10.00<br> Connected Reconstruction (parts)=3<br> Sub-scan post alignment [0]=10.000000<br> Sub-scan post alignment [1]=10.000000<br> Sub-scan post alignment [2]=10.000000<br> Sub-scan scan length [0]=1035<br> Sub-scan scan length [1]=1035<br> Sub-scan scan length [2]=1036<br> Used extra shift in X per scan(micron)= 0.000 -1.993 -4.803 <br> Used extra shift in Y per scan(micron)= 0.000 -25.239 -44.091 <br> First Section=63<br> Last Section=3495<br> Reconstruction duration per slice (seconds)=0.349107<br> Total reconstruction time (2071 slices) in seconds=723.000000<br> Section to Section Step=1<br> Sections Count=3433<br> Result File Type=TIF<br> Result File Header Length (bytes)=12<br> Result Image Width (pixels)=2152<br> Result Image Height (pixels)=2056<br> Pixel Size (µm)=6.99992<br> Reconstruction Angular Range (deg)=192.20<br> Use 180+=OFF<br> Angular Step (deg)=0.2000<br> Smoothing=3<br> Smoothing kernel=2 (Gaussian)<br> Ring Artifact Correction=20<br> Draw Scales=OFF<br> Object Bigger than FOV=OFF<br> Reconstruction from ROI=ON<br> ROI Top (pixels)=2282<br> ROI Bottom (pixels)=223<br> ROI Left (pixels)=214<br> ROI Right (pixels)=2369<br> ROI reference length=2452<br> Filter cutoff relative to Nyquist frequency=100<br> Filter type=0<br> Filter type description=Hamming (Alpha=0.54)<br> Undersampling factor=1<br> Threshold for defect pixel mask (%)=0<br> Beam Hardening Correction (%)=54<br> CS Static Rotation (deg)=78.89<br> Minimum for CS to Image Conversion=0.003750<br> Maximum for CS to Image Conversion=0.105554<br> HU Calibration=OFF<br> BMP LUT=0<br> Cone-beam Angle Horiz.(deg)=11.863247<br> Cone-beam Angle Vert.(deg)=7.950323<br> Automatic matching in Z=50<br> Automatic matching in X/Y=50<br> Automatic matching in rotation=0.000000<br> Automatic fusion=1<br> <br> Data size has been reduced by conversion from 16-bit to 8-bit and decreasing the scale of the images.</p>
µCT scan data: stack of DICOM images
<p>MicroCT or µCT scan data: stack of DICOM images of the crab <i>Secretanella</i> sp. (ALMNH:Paleo:6522) from an upper Campanian methane seep limestone in Pennington County, South Dakota.</p>
Data (µCT) to "A new species of the genus Dolichoderus Lund, 1831 (Hymenoptera: Formicidae) from a Late Eocene European amber" by Dubovikoff D. and Zharkov D. in Caucasian Entomological Bulletin
<p>This dataset is the µCT scan of the holotype ( worker, JDC10574R) of †Dolichoderus jonasi Dubovikoff & Zharkov, 2022 that was used by Dubovikoff & Zharkov in publication "Dubovikoff, D. A., Zharkov, D. M. 2022. A new species of the genus Dolichoderus Lund, 1831 (Hymenoptera: Formicidae) from a Late Eocene European amber. Caucasian Entomological Bulletin 181, 147–152 (doi:10.23885/181433262022181-147152)."</p><p>Arrays of microtomographic data were obtained at St. Petersburg State University (St. Petersburg, Russia) using a desktop high-resolution X-ray microtomograph SkyScan 1172. The holotype (JDC10574R) was scanned with the following parameters: voltage 40 kV, current 250 µA, without filter, with a pixel size of 2.46 microns and a resolution of 2848 × 2692 pixels per slice with continuous 360° rotation and a shutter speed of 1300 ms per frame (2268 X-ray projections).</p><p>The material is currently deposited in the collection of the Kaliningrad Amber Museum, Kaliningrad, Russia.</p><p> </p>
Resliced X-ray µCT scans of 17 tropical wood species – multiresolution experiment
<p>When considering X-ray µCT for identification of a wooden sample, the question remains which resolution will be sufficient to visualize the wood anatomical features. This dataset contains the X-ray µCT scans, resliced along the three wood directions (transverse, radial and tangential), of 17 different wood species at four different resolutions. These scans form the foundation of a comparative study to evaluate the success of wood anatomical description resolutions ranging from 1 to 15 µm. The dataset of 17 scanned species is made available online to serve as a first step towards a reference database of scanned wood species, facilitating and encouraging more systematic use of X-ray µCT for the identification of wood species.</p> <p>The 17 wood species studied in this paper were selected according to their occurrence among the objects of the Congolese heritage collection of the RMCA. In the past, 7% (3814 out of 55.000 objects) of the museum’s collection of wooden cultural objects was analysed and identified by the wood biology department of the RMCA. Based on this dataset of identifications (available here: 10.5281/zenodo.10671337), the most occurring wood species were selected:</p> <p>RUBIACEAE <em>Crossopteryx febrifuga</em> Afzel. Ex G. Don <br>EUPHORBIACEAE <em>Ricinodendron heudelotii </em>(Baill.) Pierre ex Heckel <br>APOCYNACEAE <em>Alstonia congensis</em> Engl. <br>BURSERACEAE <em>Canarium schweinfurthii </em>Engl. <br>RUBIACEAE <em>Nauclea pobeguinii</em> (Pobeg.) Merr. <br>VERBENACEAE <em>Vitex madiensis</em> Oliv. <br>BORAGINACEAE <em>Cordia millenii</em> Baker <br>MORACEAE<em> Milicia excelsa</em> (Welw.) C.C. Berg <br>RUBIACEAE <em>Nauclea latifolia</em> Sm. <br>BIGNONIACEAE<em> Markhamia tomentosa</em> (Benth.) K. Schum. Ex Engl. <br>FABACEAE <em>Albizia zygia</em> (DC.) J.F. Macbr. <br>FABACEAE<em> Pterocarpus tinctorius </em>Welw. <br>FABACEAE <em>Pterocarpus angolensis </em>DC. <br>APOCYNACEAE <em>Funtumia Africana</em> (Benth.) Stapf <br>MORACEAE <em>Ficus mucuso </em>Welw. ex Fical <br>VERBENACEAE <em>Vitex ferruginea</em> Schumach. & Thonn. <br>OLACACEAE <em>Strombosiopsis tetranda </em>Engl.</p> <p>Each sample was prepared for scanning by subdividing it into small cubes, tuned to the scan resolution: cubes of 1x1x10 mm for the 1µm scans; cubes of 5x5x5 mm were made for the 3µm resolution scans, and for the 8µm and 15µm scans the cubes were cut to 1x1x1 cm. The wood samples were scanned at 4 different ‘resolutions’ -more correctly the approximate voxel pitch of the scans but further referred to as resolution. The Nanowood X-ray µCT scanner was used to make the 68 scans (17 wood species at 4 resolutions). This scanner was custom-built at the UGent Centre for X-ray Tomography (www.ugct.ugent.be) and recently refurbished in collaboration with TESCAN-XRE (www.XRE.be, part of the TESCAN ORSAY HOLDINGS a.s.), a UGCT spin-off company.</p> <p>The .jpeg files in this dataset are named as follows: W<strong>ood species_Tw number_resolution_wood plane_sequence number</strong>.</p> <ul> <li>The Tw number references the 'Tervuren Wood' collection, or the Xylarium of the RMCA, which can be consulted via this website: https://www.africamuseum.be/nl/research/collections_libraries/biology/collections/xylarium</li> <li>The resolution of the scans - more correctly the approximate voxel pitch of the scans - is indicated in µm </li> <li>The three wood planes are abbreviated in the file names: transverse (xs), radial (rls), tangential (tls)</li> <li>The sequence number: for each scan, at least 3 reslices were made for each of the three wood planes. This to take full advantage of the three-dimensional nature of the scans.</li> </ul>
Owenia fusiformis µCT scan
<p>µCT scan of a specimen of <em>Owenia fusiformis</em> stained with PTA for one week. Scan and reconstruction were obtained with the following settings:</p> <p>[System]<br> Scanner=SkyScan1272<br> Instrument S/N=15H09112<br> Software Version=1.1.10<br> Source Type=HAMAMATSU_L11871_20<br> Camera Type=XIMEA xiRAY16<br> Camera Pixel Size (µm)=7.4<br> Camera X/Y Ratio=1.0058<br> <br> [Acquisition]<br> Number Of Files= 940<br> Number Of Rows= 1640<br> Number Of Columns= 2452<br> Partial Width=OFF<br> Image crop origin X=0<br> Image crop origin Y=0<br> Camera binning=2x2<br> Image Rotation=-0.00100<br> Optical Axis (line)= 932<br> Camera to Source (mm)=274.64085<br> Object to Source (mm)=50.22367<br> Source Voltage (kV)= 45<br> Source Current (µA)= 165<br> Image Pixel Size (µm)=2.706481<br> Scaled Image Pixel Size (µm)=2.706481<br> Image Format=TIFF<br> Depth (bits)=16<br> Reference Intensity=57000<br> Exposure (ms)=1166<br> Rotation Step (deg)=0.200<br> Use 360 Rotation=NO<br> Scanning position=12.126 mm<br> Frame Averaging=ON (3)<br> Random Movement=OFF (15)<br> Flat Field Correction=ON<br> FF updating interval=94<br> Geometrical Correction=ON<br> Filter=No Filter<br> Gantry direction=CC<br> Rotation Direction=CC<br> Type of Detector Motion=STEP AND SHOOT<br> Scanning Trajectory=ROUND<br> Number Of Horizontal Offset Positions=1<br> Number of connected scans=5<br> Current scan number=1<br> Number of lines to be reconstructed=1290<br> Scan duration=1h:16m:33s<br> Maximum vertical TS=5.0<br> [Reconstruction]<br> Reconstruction Program=NRecon<br> Program Version=Version: 1.7.1.0<br> Reconstruction engine=InstaRecon<br> Engine version=Version: 2.0.3.7<br> Reconstruction from batch=Yes<br> Postalignment=5.50<br> Connected Reconstruction (parts)=5<br> Sub-scan post alignment [0]=-0.500000<br> Sub-scan post alignment [1]=3.000000<br> Sub-scan post alignment [2]=5.500000<br> Sub-scan post alignment [3]=5.500000<br> Sub-scan post alignment [4]=9.000000<br> Sub-scan scan length [0]=1292<br> Sub-scan scan length [1]=1290<br> Sub-scan scan length [2]=1292<br> Sub-scan scan length [3]=1289<br> Sub-scan scan length [4]=1290<br> Used extra shift in X per scan(micron)= 0.000 9.266 21.355 35.921 42.377 <br> Used extra shift in Y per scan(micron)= 0.000 -18.235 -28.164 -29.070 -33.034 <br> Reconstruction servers= SKYSCAN1272 <br> First Section=359<br> Last Section=5289<br> Reconstruction duration per slice (seconds)=0.298839<br> Total reconstruction time (3875 slices) in seconds=1158.000000<br> Section to Section Step=1<br> Sections Count=4931<br> Result File Type=TIF<br> Result File Header Length (bytes)=12<br> Result Image Width (pixels)=2252<br> Result Image Height (pixels)=2220<br> Pixel Size (µm)=2.70648<br> Reconstruction Angular Range (deg)=188.00<br> Use 180+=OFF<br> Angular Step (deg)=0.2000<br> Smoothing=3<br> Smoothing kernel=2 (Gaussian)<br> Ring Artifact Correction=28<br> Draw Scales=OFF<br> Object Bigger than FOV=OFF<br> Reconstruction from ROI=ON<br> ROI Top (pixels)=2305<br> ROI Bottom (pixels)=82<br> ROI Left (pixels)=117<br> ROI Right (pixels)=2369<br> ROI reference length=2452<br> Filter cutoff relative to Nyquist frequency=100<br> Filter type=0<br> Filter type description=Hamming (Alpha=0.54)<br> Undersampling factor=1<br> Threshold for defect pixel mask (%)=0<br> Beam Hardening Correction (%)=64<br> CS Static Rotation (deg)=0.00<br> Minimum for CS to Image Conversion=0.038815<br> Maximum for CS to Image Conversion=0.506935<br> HU Calibration=OFF<br> BMP LUT=0<br> Cone-beam Angle Horiz.(deg)=7.559776<br> Cone-beam Angle Vert.(deg)=5.060350<br> Automatic matching in Z=50<br> Automatic matching in X/Y=50<br> Automatic matching in rotation=0.000000<br> Automatic fusion=1<br> </p> <p>Data size has been reduced by conversion from 16-bit to 8-bit and decreasing the scale of the images.</p>
"Onset of post-cratering melting of target rocks at the impact melt contact: observations from the Vredefort impact structure, South Africa" µCT data
<p>µCT Dataset. </p>
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