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Advanced Training

Equipment: Xradia MicroXCT-400
Trainer: Tiffany Fong of Xradia
Dates: 18-20 May 2010

Key-points of Advanced training

Sample Prep
  1. Biological samples which are usually kept in solution during storage must be scanned in liquid. Otherwise there is shrinking of tissues during the long scan and this causes significant artifact. The source-drift image (captured when using Recipes) shows if there has been shrinking.
  1. Follow the updated MicroCT manual to set up the scan, especially the steps in setting up Tomography:
    • Always start with 80 keV, 8W. Adjust exposure time so that photon counts are between 5000 and 20000.
    • Do filter selection using Table in manual
    • Adjust voltage so that in reference corrected projection image, counts are between 0.23 and 0.35

  2. Stable X-ray voltage range for MicroCT is 40-90 keV (though lower is allowed)

  3. Filters to correct beam-hardening were recommended. There are 2 series of filters in the kit provided by Xradia - LE for biological samples etc., HE for semiconductor samples etc.
    • Optionally use microscopic glass slides taped to source. **

  4. For a tomography, acquire between 300 to 2000 to as much as 6000 images. Not necessary to have odd number of images or to have multiples of 180.

  5. -90 to +90 degrees may not be enough as there are some missing areas due to cone angle (Cone Angle Defect Correction). Few extra projections (e.g. -93 to 93 degrees) can remove this error. The calculation for this can be done in 2 ways:
    • Go to Microscope >> Calculate Optimum...
    • For a tomography setting, if we click on Recipes button, the angles are automatically updated

  6. Xradia Trainer recommended to do full 360 degree tomography (Start angle = -180 degree, End angle = 180 degrees). However our MicroCT currently does not allow 360 degree rotation, and it is OK to use 180 degree or rotation recommended after Microscope >> Calculate Optimum...

  7. In Microscope >> Configure Settings, always keep Dynamic Ring Removal clicked ON as this removes Ring artifacts. This is ON by default.

  8. Always better to use Recipe option as it covers most of the required pre-acquisition steps

  9. Using Recipes option for tomography acquires a Source Drift file (acquires the zero-degree projection repeatedly after every 60 frames) - this can be manually viewed to see whether sample underwent internal change during scan (possible for biological samples) or external change (e.g. sample tilted). Also X-ray source may have drifted which can be corrected later.

  10. OK to use binning of 2 while acquiring.

  11. To center the sample (i.e. to find isocenter) - quick method (takes 2 minutes)
    • Crosshair on image can be useful. Activate by Microscope >> Highlight Center FOV
    • Double click on center in low mag (at 0 degree projection) to get X-centering
    • Double click on center in low mag (at -90 degree projection) to get Z-centering
    • Choose Y-position based on sample

  12. Switch on keyboard console can move sample from 0 to -90 degree or vice versa in 1 click.

  13. Joystick on keyboard console can move sample in X, Y, Z. Up and down (Y) is very useful.

  14. Source and Detector Distance
    • For all objectives except Half-X, bring Source and Detector as close as possible. We achieved same quality as 30 hour scan in 2 hours by reducing source, detector distance from rotation axis from 40mm to 3mm.
    • For Half-X, bring source close. Keep detector far (~100m)
    • For Phase contrast, keep source far (~100mm). Keep detector close. 
Special Tomography
  1. Using Recipes, easy to do multiple scans of the same sample. We just need to click different isocenters.

  2. Also possible to stitch these volumes together to form a larger volume (longer in the Y-dimension). For this, the Y-distance between 2 adjacent tomographies should allow for some overlap.
    The maximum Y-distance is calculated using the EXCEL file:
    <<SrcDetCalculator.exe>> which is kept in the PC.

    • Can set variable exposure times to adjust for different lengths of sample along Zero and 90 degree direction.
    • Can set this in the TEXT file:
    • Rename the file to be used to <<ExposureTable>>
    • Then go to
      Recipes >> Apply Exp. Time Correction
    • Can set our own times e.g.
      90 degree : 4 sec
      0 degree: 1 sec
      Then use a cosine formula to fit this curve.
  1. Find best Beam-Hardening constant (between 0 and 1.0 usually) using same tool as for Center Shift. Use Line Profile to find out optimum value of parameter.

  2. In Reconstructor Settings dialog, disable Defect Correction

  3. In Reconstructor Settings dialog, use Recon filters to smooth 2D projections before Reconstruction to reduce impact of noise. Usually smoothing filter of 0.5 is used. Can use more for 40x where data is more noisy.

  4. OK to use binning of 1 while reconstructing.

  5. In Reconstructor Settings dialog, disable Dark Spots option.

  6. In Reconstructor Settings dialog, reduction of reconstruction area is possible (by using lines on the slices shown)

  7. Always correct for Source Drift before Recon. To do this, go to:
    Plugins >> Source Drift

  8. Scaling of CT Data
    1. Water Phantoms provided for 0.5x, 4x, 10x (in holder with Red caps)
      • After scanning water phantoms, in TXM-Controller, open the Tomography file, select a Circular region inside the water phantom. Then go to:
        ROI Statistics >> Mean 
      • Select the mean for water (e.g. 33740)
      • Select the mean for air (e.g. 18400)
    2. Now do reconstruction of any volume (which had same objectives) with the selected CT-Scale Filter.
    3. Each CT-Scale Filter should have 4 parameters e.g.
  1. Can use the following plugins for Reconstructed Volume files by opening them in TXM Controller
    Microscope >> Plugins >>
    • Motion Artifact Reduction
       - **
    • Stitch 2 volumes
       - center shift, beam hardening should be same between volumes
    • Crop Fill
       - switch to Absorption mode by going to
         Image Toolbox >> Reference >> Absorption mode
       - use this for Circular apertures (like 0.5x)
       - before doing this, do kernel smoothing of 0.5 to reduce noise

  2. Filtering of 3D images may be done (in TXM Controller) to reduce noise

** more information to be added