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