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.