Tomogram quality assessment

To visually asses the quality of a final tomogram reconstruction, we recommend to look closely at the gold beads in the volume. A good tilt series alignment and therefore a good tomogram reconstruction results in perfectly symmetric gold beads, as shown in the picture below:

Left: A good alignment results in perfectly symmetric beads. In the Y-view, the missing wedge causes an X-shape going straight through the center of the bead. In the Z-view, the beads show symmetric white "wings". Right: A bad alignment causes asymmetries and results in curved or distorted shapes in both views.

It can always be that a few gold beads on the border of the tomogram or close to the carbon show bad alignment. If, however, your tomogram shows many gold beads that indicate a bad alignment we recommend the following:

• Go back to the tilt series alignment step and make sure that no mistakes were made. Consider following these guidelines if you were using IMOD for the tilt series alignment.
• Sometimes, selecting only gold beads close to the region of interest in the tomogram shows an improvement in alignment for this specific region. However, this is only feasible if the region of interest is small (e.,g., one single vesicle).