For “Coarse Alignment Not Started”:

  1. Click on “Calculate Cross-Correlation” and wait.
  2. Click on the “A” next to “Newstack”. The section under “Newstack” will enlarge.
  3. Click the up-button next to “Coarse aligned image stack binning” and change it to 4.
    1. this step can speed up the process, but doesn’t really affect the resulted tomogram. It’s fine if you forget to do it.
  4. Check “Reduce size with antialiasing filter” and the rest two choices should remain checked.
  5. Click “Generate Coarse Aligned Stack”.
  6. Click “Done”. Then similar effect as step 5 above will occur, and you are in “Fiducial Model Gen.” Block.