DOI: 10.5281/zenodo.5222920
title: Owenia fusiformis µCT scan

description: 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: [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> Data size has been reduced by conversion from 16-bit to 8-bit and decreasing the scale of the images.