With the correlation wizard you can correlate the images of the LM and SEM. Note that we do not recommend to perform this correlation for SEM images acquired with the Atlas Array Tomography module. The wizard contains the following 4 steps:

  • Import Z-Stacks
  • Correlation
  • Manual Correction
  • Create Final Correlation Image
  1. In the CAT tool click on Start Correlation Wizard.
  2. You will see the first step Import Z-Stacks.
  3. Click on Left Container to load the aligned z-stack image from the SEM.
  4. Click on Right Container to load the aligned z-stack image from the LM.
  5. Click on Next.
  6. You will see step 2/4 Correlation.
  7. Under Transform decide whether you want to transform the Left Z-Stack into the Right Z-Stack or vice versa.
  8. Under Mode select 4 Points.
  9. Click on Set Points.
  10. Set the first 3 correlation points in the first Z-Stack image of the left image.
  11. Set the corresponding 3 correlation points in the first Z-Stack image of the right image.
  12. After the third point in the right image was set, the software automatically jumps to the last Z-Stack image.
  13. Set the fourth correlation point in the left image first and then set it in the right image.
  14. Click on Create correlated Z-Stack.
  15. The correlated Z-Stack image will be generated and displayed in a separate image container.
  16. Click on Next.
  17. You will see step 3/4 Manual Correction.
  18. In this step you can manually correct the alignment of the images by moving and/or rotating the images according to each other. To rotate the image use the handle at the top of the image frame. To move the image simply left click on the image and hold the mouse button pressed while moving the image.
  19. If you finished the alignment of an image click on Accept. You can browse through the correlated Z-Stack images by using the Z-Position slider in the Dimension tab.
  20. Click on Next.
  21. You will see step 4/4 Create Final Correlation Image.
  22. Click on Create Final Z-Stack.
  23. The correlated Z-Stack image will be created.
  24. Click on Finish to exit the wizard.
  1. You have successfully created a correlated Z-Stack image.