For “Pre-processing Not Started”:

1. Click on “Pre-processing”. Then the window should change and the red “Pre-processing” block should become fuchsia, indicating you are doing process in this block.
2. Click on “Find X-rays (Trial Mode)” and wait for it to finish. If you want to know what it does, move your mouse to that button and stay there. A small pop-up window will tell you the function. This applies to all the buttons in etomo.
3. Click “Create Fixed Stack”, then wait.
4. Click “Use Fixed Stack”.
5. Click “Done”. Then the fuchsia “Pre-processing In Progress” should turn green, and the window will change. Now, you are inside the “Coarse Alignment” block.