Analysis of X-ray CT Calibration Spheres using the Metrology Workroom

Introduction

This tutorial provides a step-by-step guide on how to analyze calibration spheres used in X-ray Computed Tomography (CT) using the Metrology Workroom in Amira-Avizo software. Understanding this process is crucial for ensuring accurate measurements and improving the efficiency of your CT data analysis.

Step 1: Load the CT Data

• Gather your data files, which can be in either TIFF stack or raw volume formats.
• Ensure to use the effective pixel size from the CT scan properties. For this example, the effective pixel size is 16 microns.
• Load the data into the project view.

Step 2: Verify the Quality of the CT Scan

• Use the ortho slice view to assess the scan quality.
• Check for:
  • Good contrast between the spheres and background.
  • Presence of all spheres intended for analysis.
  • Absence of reconstruction artifacts (e.g., ring artifacts or streaking).
• Confirm that the spheres are fully contained within the volume using volume rendering.

Step 3: Access the Metrology Workroom

• Navigate to the Metrology Workroom from the toolbar at the top of the screen.
• Familiarize yourself with the layout, which includes control tools on the left and viewing windows on the right.

Step 4: Extract Surface Profiles

• Select the raw data for the calibration target from the dropdown menu.
• Choose the adaptive subvoxel method for surface profile extraction. Note that this process may take a few minutes.
• After the surface fitting is complete, check the results using the ortho slice view.

Step 5: Profile the Spheres

• Switch to the 3D viewing window and select one of the spheres.
• Avoid areas with CT artifacts by repositioning the sphere.
• Open the geometries window and select the sphere fitting tab.
• Click on various points around the surface of the sphere to create a fitting. Ensure the points are evenly distributed.
• If satisfied with the fitting, click on "Finish." The properties, such as the radius, will display in the geometries window.

Step 6: Measure Distances Between Sphere Centers

• Zoom out to view the calibration target and select the second sphere.
• Repeat the sphere profiling process for the second sphere.
• To measure the distance between the centers of the spheres:
  • Right-click on the metrology tab and select "Measures."
  • Choose "Dimensional Measures" and then "Distances."
  • Select the centers of the two spheres you wish to measure.
• Click "Create" to generate the distance measure, which will display in the viewing windows.

Step 7: Record and Export Measurements

• The distance between the two sphere centers will be shown (e.g., 29.671 millimeters).
• Adjust annotations such as line width, cone size, and colors as desired.
• Click "Finish" to save the measurements.
• For multiple spheres, repeat the measurement process as needed.
• To export the data, navigate to the top right corner and select the export option to create a spreadsheet of measures.

Conclusion

In this tutorial, you learned how to analyze X-ray CT calibration spheres using the Metrology Workroom in Amira-Avizo software. Key steps included loading data, verifying scan quality, extracting surface profiles, measuring distances, and exporting results. These processes ensure precise measurements and improve your analysis efficiency. For further applications, consider recalibrating voxel sizes based on the distance measurements obtained.