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11 results for “µCT scanning”

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zenodo40/100

Cryptolacruma nidis (Isopoda: Epicaridea), Kachin amber, PED 0226, µCT scan

Two fossil specimens preserved in Kachin amber (Myanmar, mid-Cretateous), described as Cryptolacruma nidis 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.

opencc-by-4.0Oct 2022View details →

zenodo40/100

Nerocila acuminata head µCT scan

Nerocila acuminata 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). 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 µm3 voxel size.

opencc-by-4.0Aug 2022View details →

zenodo36/100

Euphrosine foliosa µCT-scan

Image sequence of a reconstructed µCT-scan of Euphrosine foliosa AUDOUIN & MILNE EDWARDS 1833 performed with the following settings   [System] Scanner=SkyScan1272 Instrument S/N=15H09112 Software Version=1.1.10 Source Type=HAMAMATSU_L11871_20 Camera Type=XIMEA xiRAY16 Camera Pixel Size (um)=7.4 Camera X/Y Ratio=1.0058 Number Of Files=  482 Number Of Rows= 1092 Number Of Columns= 1632 Partial Width=OFF Image crop origin X=0 Image crop origin Y=0 Camera binning=3x3 Image Rotation=0.01800 Optical Axis (line)=  593 Camera to Source (mm)=174.64085 Object to Source (mm)=62.93450 Source Voltage (kV)=  60 Source Current (µA)= 166 Image Pixel Size (µm)=8.000109 Scaled Image Pixel Size (µm)=8.000109 Image Format=TIFF Depth (bits)=16 Reference Intensity=57000 Exposure (ms)=741 Rotation Step (deg)=0.400 Use 360 Rotation=NO Scanning position=16.028 mm Frame Averaging=ON (6) Random Movement=OFF (15) Flat Field Correction=ON FF updating interval=161 Geometrical Correction=ON Filter=Al 0.25mm Gantry direction=CC Rotation Direction=CC Type of Detector Motion=STEP AND SHOOT Scanning Trajectory=ROUND Number Of Horizontal Offset Positions=1 Number of connected scans=3 Current scan number=1 Number of lines to be reconstructed=732 Study Date and Time=28 Jun 2019  12h:28m:47s Scan duration=0h:44m:47s Maximum vertical TS=5.0 [Reconstruction] Reconstruction Program=NRecon Program Version=Version: 1.7.1.0 Reconstruction engine=InstaRecon Engine version=Version: 2.0.3.7 Reconstruction from batch=No Postalignment=7.00 Connected Reconstruction (parts)=3 Sub-scan post alignment [0]=8.000000 Sub-scan post alignment [1]=7.000000 Sub-scan post alignment [2]=7.000000 Sub-scan scan length [0]=731 Sub-scan scan length [1]=731 Sub-scan scan length [2]=732 Used extra shift in X per scan(micron)= 0.000  -1.262  4.411  Used extra shift in Y per scan(micron)= 0.000  -9.915  -43.932  First Section=175 Last Section=2340 Reconstruction duration per slice (seconds)=0.110048 Total reconstruction time (1463 slices) in seconds=161.000000 Section to Section Step=1 Sections Count=2166 Result File Type=TIF Result File Header Length (bytes)=12 Result Image Width (pixels)=840 Result Image Height (pixels)=656 Pixel Size (um)=8.00011 Reconstruction Angular Range (deg)=192.80 Use 180+=OFF Angular Step (deg)=0.4000 Smoothing=1 Smoothing kernel=2 (Gaussian) Ring Artifact Correction=5 Draw Scales=OFF Object Bigger than FOV=OFF Reconstruction from ROI=ON ROI Top (pixels)=1182 ROI Bottom (pixels)=523 ROI Left (pixels)=420 ROI Right (pixels)=1263 ROI reference length=1632 Filter cutoff relative to Nyquist frequency=100 Filter type=0 Filter type description=Hamming (Alpha=0.54) Undersampling factor=1 Threshold for defect pixel mask (%)=0 Beam Hardening Correction (%)=40 CS Static Rotation (deg)=5.96 Minimum for CS to Image Conversion=0.004763 Maximum for CS to Image Conversion=0.219915 HU Calibration=OFF BMP LUT=0 Cone-beam Angle Horiz.(deg)=11.844029 Cone-beam Angle Vert.(deg)=7.940657 Automatic matching in Z=50 Automatic matching in X/Y=50 Automatic matching in rotation=0.000000 Automatic fusion=1

opencc-by-4.0Aug 2021View details →

zenodo36/100

Two fossil isopods from the Middle Jurassic of Bielefeld ES/jb-30755 and ES/jb-30756 µCT scan

Two fossil specimens belonging to the group Isopoda, Middle Jurassic, Bajocian, Parkinsonia parkinsoni Zone, quarry "Bethel 1", Bielefeld, Germany, deposited at the Natural History Museum Bielefeld, accession numbers ES/jb-30755 and ES/jb-30756. X-ray µCT scan, performed using a Phoenix (GE Sensing & Inspection Technologies GmbH) Nanotom M scanner, 120 kV,  100 µA, 18.4464 µm3 voxel size.

opencc-by-4.0Aug 2022View details →

zenodo36/100

Fossil isopod from the Lower Jurassic of Kircheim unter Teck GPIT-PV-76948 µCT scan

One fossil specimen of the group Isopoda, described as Palaega suevica 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. X-ray µCT scan, performed using a Phoenix (GE Sensing & Inspection Technologies GmbH) Nanotom M scanner, 120 kV,  100 µA, 4.55246 µm3 voxel size.

opencc-by-4.0Aug 2022View details →

zenodo36/100

Fossil isopod from the Middle Jurassic of Bielefeld ES/jb-8744 µCT scan

One fossil specimen belonging to the group Isopoda, Middle Jurassic, Bajocian, Parkinsonia parkinsoni Zone, quarry "Bethel 1", Bielefeld, Germany, deposited at the Natural History Museum Bielefeld, accession number ES/jb-8744. X-ray µCT scan, performed using a Phoenix (GE Sensing & Inspection Technologies GmbH) Nanotom M scanner, 120 kV,  100 µA, 13.86661 µm3 voxel size.

opencc-by-4.0Aug 2022View details →

zenodo32/100

Magelona mirabilis µCT scan

µCT scan of a specimen of Magelona mirabilis stained with PTA for one week. Scan and reconstruction were obtained with the following settings: [System] Scanner=SkyScan1272 Instrument S/N=15H09112 Software Version=1.1.10 Source Type=HAMAMATSU_L11871_20 Camera Type=XIMEA xiRAY16 Camera Pixel Size (µm)=7.4 Camera X/Y Ratio=1.0058 [Acquisition] Filename Index Length=8 Number Of Files=  940 Number Of Rows= 1640 Number Of Columns= 2452 Partial Width=OFF Image crop origin X=0 Image crop origin Y=0 Camera binning=2x2 Image Rotation=0.00400 Optical Axis (line)=  932 Camera to Source (mm)=274.64085 Object to Source (mm)=55.67001 Source Voltage (kV)=  60 Source Current (µA)= 166 Image Pixel Size (µm)=2.999977 Scaled Image Pixel Size (µm)=2.999977 Image Format=TIFF Depth (bits)=16 Reference Intensity=57000 Exposure (ms)=2832 Rotation Step (deg)=0.200 Use 360 Rotation=NO Scanning position=2.271 mm Frame Averaging=ON (4) Random Movement=OFF (8) Flat Field Correction=ON FF updating interval=55 Geometrical Correction=ON Filter=Al 0.25mm Gantry direction=CC Rotation Direction=CC Type of Detector Motion=STEP AND SHOOT Scanning Trajectory=ROUND Number Of Horizontal Offset Positions=1 Number of connected scans=3 Current scan number=1 Number of lines to be reconstructed=1093 Scan duration=3h:17m:30s Maximum vertical TS=5.0 [Reconstruction] Reconstruction Program=NRecon Program Version=Version: 1.7.1.0 Reconstruction engine=InstaRecon Engine version=Version: 2.0.3.7 Reconstruction from batch=No Postalignment=9.50 Connected Reconstruction (parts)=3 Sub-scan post alignment [0]=8.500000 Sub-scan post alignment [1]=9.000000 Sub-scan post alignment [2]=9.500000 Sub-scan scan length [0]=1091 Sub-scan scan length [1]=1093 Sub-scan scan length [2]=1093 Used extra shift in X per scan(micron)= 0.000  -1.327  0.089  Used extra shift in Y per scan(micron)= 0.000  -13.707  -21.439  Time and Date=Jul 14, 2021  12:03:18 First Section=315 Last Section=3430 Reconstruction duration per slice (seconds)=0.294737 Total reconstruction time (2185 slices) in seconds=644.000000 Section to Section Step=1 Sections Count=3116 Result File Type=TIF Result File Header Length (bytes)=12 Result Image Width (pixels)=1960 Result Image Height (pixels)=1960 Pixel Size (µm)=2.99998 Reconstruction Angular Range (deg)=188.00 Use 180+=OFF Angular Step (deg)=0.2000 Smoothing=0 Ring Artifact Correction=8 Draw Scales=OFF Object Bigger than FOV=OFF Reconstruction from ROI=ON ROI Top (pixels)=2115 ROI Bottom (pixels)=153 ROI Left (pixels)=194 ROI Right (pixels)=2156 ROI reference length=2452 Filter cutoff relative to Nyquist frequency=100 Filter type=0 Filter type description=Hamming (Alpha=0.54) Undersampling factor=1 Threshold for defect pixel mask (%)=0 Beam Hardening Correction (%)=0 CS Static Rotation (deg)=0.00 Minimum for CS to Image Conversion=-0.039105 Maximum for CS to Image Conversion=0.529521 HU Calibration=OFF BMP LUT=0 Cone-beam Angle Horiz.(deg)=7.559778 Cone-beam Angle Vert.(deg)=5.060351 Automatic matching in Z=50 Automatic matching in X/Y=50 Automatic matching in rotation=0.000000 Automatic fusion=1   Data size has been reduced by conversion from 16-bit to 8-bit and decreasing the scale of the images.

opencc-by-4.0Nov 2021View details →

zenodo32/100

Sternaspis scutata µCT scan

µCT scan of a specimen of Sternaspis scutata stained with PTA for one week. Scan and reconstruction were obtained with the following settings: [System] Scanner=SkyScan1272 Instrument S/N=15H09112 Software Version=1.1.10 Source Type=HAMAMATSU_L11871_20 Camera Type=XIMEA xiRAY16 Camera Pixel Size (µm)=7.4 Camera X/Y Ratio=1.0058 [Acquisition] Number Of Files=  961 Number Of Rows= 1640 Number Of Columns= 2452 Partial Width=OFF Image crop origin X=0 Image crop origin Y=0 Camera binning=2x2 Image Rotation=-0.00100 Optical Axis (line)=  890 Camera to Source (mm)=174.64085 Object to Source (mm)=82.59950 Source Voltage (kV)=  70 Source Current (µA)= 142 Image Pixel Size (µm)=6.999924 Scaled Image Pixel Size (µm)=6.999924 Image Format=TIFF Depth (bits)=16 Reference Intensity=57000 Exposure (ms)=1238 Rotation Step (deg)=0.200 Use 360 Rotation=NO Scanning position=11.719 mm Frame Averaging=ON (4) Random Movement=OFF (15) Flat Field Correction=ON FF updating interval=120 Geometrical Correction=ON Filter=Al 0.5mm Gantry direction=CC Rotation Direction=CC Type of Detector Motion=STEP AND SHOOT Scanning Trajectory=ROUND Number Of Horizontal Offset Positions=1 Number of connected scans=3 Current scan number=1 Number of lines to be reconstructed=1036 Scan duration=1h:40m:36s Maximum vertical TS=5.0 [Reconstruction] Reconstruction Program=NRecon Program Version=Version: 1.7.1.0 Reconstruction engine=InstaRecon Engine version=Version: 2.0.3.7 Reconstruction from batch=Yes Postalignment=10.00 Connected Reconstruction (parts)=3 Sub-scan post alignment [0]=10.000000 Sub-scan post alignment [1]=10.000000 Sub-scan post alignment [2]=10.000000 Sub-scan scan length [0]=1035 Sub-scan scan length [1]=1035 Sub-scan scan length [2]=1036 Used extra shift in X per scan(micron)= 0.000  -1.993  -4.803  Used extra shift in Y per scan(micron)= 0.000  -25.239  -44.091  First Section=63 Last Section=3495 Reconstruction duration per slice (seconds)=0.349107 Total reconstruction time (2071 slices) in seconds=723.000000 Section to Section Step=1 Sections Count=3433 Result File Type=TIF Result File Header Length (bytes)=12 Result Image Width (pixels)=2152 Result Image Height (pixels)=2056 Pixel Size (µm)=6.99992 Reconstruction Angular Range (deg)=192.20 Use 180+=OFF Angular Step (deg)=0.2000 Smoothing=3 Smoothing kernel=2 (Gaussian) Ring Artifact Correction=20 Draw Scales=OFF Object Bigger than FOV=OFF Reconstruction from ROI=ON ROI Top (pixels)=2282 ROI Bottom (pixels)=223 ROI Left (pixels)=214 ROI Right (pixels)=2369 ROI reference length=2452 Filter cutoff relative to Nyquist frequency=100 Filter type=0 Filter type description=Hamming (Alpha=0.54) Undersampling factor=1 Threshold for defect pixel mask (%)=0 Beam Hardening Correction (%)=54 CS Static Rotation (deg)=78.89 Minimum for CS to Image Conversion=0.003750 Maximum for CS to Image Conversion=0.105554 HU Calibration=OFF BMP LUT=0 Cone-beam Angle Horiz.(deg)=11.863247 Cone-beam Angle Vert.(deg)=7.950323 Automatic matching in Z=50 Automatic matching in X/Y=50 Automatic matching in rotation=0.000000 Automatic fusion=1 Data size has been reduced by conversion from 16-bit to 8-bit and decreasing the scale of the images.

opencc-by-4.0Feb 2022View details →

zenodo32/100

µCT scan data: stack of DICOM images

MicroCT or µCT scan data: stack of DICOM images of the crab Secretanella sp. (ALMNH:Paleo:6522) from an upper Campanian methane seep limestone in Pennington County, South Dakota.

opencc-by-4.0Feb 2023View details →

zenodo28/100

Resliced X-ray µCT scans of 17 tropical wood species – multiresolution experiment

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. 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: RUBIACEAE Crossopteryx febrifuga Afzel. Ex G. Don EUPHORBIACEAE Ricinodendron heudelotii (Baill.) Pierre ex Heckel  APOCYNACEAE Alstonia congensis Engl. BURSERACEAE Canarium schweinfurthii Engl. RUBIACEAE Nauclea pobeguinii (Pobeg.) Merr. VERBENACEAE Vitex madiensis Oliv. BORAGINACEAE Cordia millenii Baker MORACEAE Milicia excelsa (Welw.) C.C. Berg  RUBIACEAE Nauclea latifolia Sm.  BIGNONIACEAE Markhamia tomentosa (Benth.) K. Schum. Ex Engl. FABACEAE Albizia zygia (DC.) J.F. Macbr. FABACEAE Pterocarpus tinctorius Welw. FABACEAE Pterocarpus angolensis DC. APOCYNACEAE Funtumia Africana (Benth.) Stapf MORACEAE Ficus mucuso Welw. ex Fical VERBENACEAE Vitex ferruginea Schumach. & Thonn. OLACACEAE Strombosiopsis tetranda Engl. 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. The .jpeg files in this dataset are named as follows: Wood species_Tw number_resolution_wood plane_sequence number. <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>

opencc-by-4.0Feb 2024View details →

zenodo28/100

Owenia fusiformis µCT scan

µCT scan of a specimen of Owenia fusiformis stained with PTA for one week. Scan and reconstruction were obtained with the following settings: [System] Scanner=SkyScan1272 Instrument S/N=15H09112 Software Version=1.1.10 Source Type=HAMAMATSU_L11871_20 Camera Type=XIMEA xiRAY16 Camera Pixel Size (µm)=7.4 Camera X/Y Ratio=1.0058 [Acquisition] Number Of Files=  940 Number Of Rows= 1640 Number Of Columns= 2452 Partial Width=OFF Image crop origin X=0 Image crop origin Y=0 Camera binning=2x2 Image Rotation=-0.00100 Optical Axis (line)=  932 Camera to Source (mm)=274.64085 Object to Source (mm)=50.22367 Source Voltage (kV)=  45 Source Current (µA)= 165 Image Pixel Size (µm)=2.706481 Scaled Image Pixel Size (µm)=2.706481 Image Format=TIFF Depth (bits)=16 Reference Intensity=57000 Exposure (ms)=1166 Rotation Step (deg)=0.200 Use 360 Rotation=NO Scanning position=12.126 mm Frame Averaging=ON (3) Random Movement=OFF (15) Flat Field Correction=ON FF updating interval=94 Geometrical Correction=ON Filter=No Filter Gantry direction=CC Rotation Direction=CC Type of Detector Motion=STEP AND SHOOT Scanning Trajectory=ROUND Number Of Horizontal Offset Positions=1 Number of connected scans=5 Current scan number=1 Number of lines to be reconstructed=1290 Scan duration=1h:16m:33s Maximum vertical TS=5.0 [Reconstruction] Reconstruction Program=NRecon Program Version=Version: 1.7.1.0 Reconstruction engine=InstaRecon Engine version=Version: 2.0.3.7 Reconstruction from batch=Yes Postalignment=5.50 Connected Reconstruction (parts)=5 Sub-scan post alignment [0]=-0.500000 Sub-scan post alignment [1]=3.000000 Sub-scan post alignment [2]=5.500000 Sub-scan post alignment [3]=5.500000 Sub-scan post alignment [4]=9.000000 Sub-scan scan length [0]=1292 Sub-scan scan length [1]=1290 Sub-scan scan length [2]=1292 Sub-scan scan length [3]=1289 Sub-scan scan length [4]=1290 Used extra shift in X per scan(micron)= 0.000  9.266  21.355  35.921  42.377  Used extra shift in Y per scan(micron)= 0.000  -18.235  -28.164  -29.070  -33.034  Reconstruction servers= SKYSCAN1272  First Section=359 Last Section=5289 Reconstruction duration per slice (seconds)=0.298839 Total reconstruction time (3875 slices) in seconds=1158.000000 Section to Section Step=1 Sections Count=4931 Result File Type=TIF Result File Header Length (bytes)=12 Result Image Width (pixels)=2252 Result Image Height (pixels)=2220 Pixel Size (µm)=2.70648 Reconstruction Angular Range (deg)=188.00 Use 180+=OFF Angular Step (deg)=0.2000 Smoothing=3 Smoothing kernel=2 (Gaussian) Ring Artifact Correction=28 Draw Scales=OFF Object Bigger than FOV=OFF Reconstruction from ROI=ON ROI Top (pixels)=2305 ROI Bottom (pixels)=82 ROI Left (pixels)=117 ROI Right (pixels)=2369 ROI reference length=2452 Filter cutoff relative to Nyquist frequency=100 Filter type=0 Filter type description=Hamming (Alpha=0.54) Undersampling factor=1 Threshold for defect pixel mask (%)=0 Beam Hardening Correction (%)=64 CS Static Rotation (deg)=0.00 Minimum for CS to Image Conversion=0.038815 Maximum for CS to Image Conversion=0.506935 HU Calibration=OFF BMP LUT=0 Cone-beam Angle Horiz.(deg)=7.559776 Cone-beam Angle Vert.(deg)=5.060350 Automatic matching in Z=50 Automatic matching in X/Y=50 Automatic matching in rotation=0.000000 Automatic fusion=1   Data size has been reduced by conversion from 16-bit to 8-bit and decreasing the scale of the images.

opencc-by-4.0Aug 2021View details →

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dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

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behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

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Last verified 2026-04-29Open record