Viterbi Alignment

Viterbi Alignment is a constrained subtomogram alignment algorithm that was introduced in our work. It imposes longitudinal constraints between neighboring molecules and optimize the alignment score using the Viterbi algorithm.

Since Viterbi Alignment only consider the longitudinal constraints, all the molecules are split into each protofilament and aligned independently in parallel.

Run Viterbi Alignment on a Landscape

API: run_viterbi_on_landscape

GUI: Subtomogram Averaging > Landscape > Run Viterbi alignment on landscape

List of Parameters

1. Select the landscape in the "landscape layer" combobox.
2. "Longitudinal range (nm)" is the constrant of the longitudinal distance between neighboring molecules.
3. "Maximum angle (deg)" is the another constraint. It is the maximum allowed angle between the spline tangent and the vector connecting the two molecules.

Run Viterbi Alignment without Constructing a Landscape

API: align_all_viterbi

GUI: Subtomogram Averaging > Alignment > Viterbi Alignment