Alignment of fiducial marks in a tomographic tilt series with an unknown rotation axis Original Research Article

Alignment for tomography using a transmission electron microscopy frequently uses colloidal gold particles as fiducial reference marks. Typically, there is an implicit assumption that the tilt axis of the tomographic series is orthogonal to the beam direction. However, this may not be true, either intentionally, if a tilt-rotate stage is used, or unintentionally, because of mechanical errors in the rotation stage or the sample fixture. Here, we provide a computer code which takes as input a set of two-dimensional (2D) observations of fiducial reference marks at various tilt angles and the values of those tilt angles. It produces as output a three-dimensional model of the observations, 2D shifts for each view, and the tilt axis direction.