The whole process of subtomogram averaging can be broadly divided into three blocks.
preprocessing block transforms experimental 2D micrographs into 3D reconstructions of an imaged region. The
particle-picking block generates putative positions and orientations for objects of interest within each volume as well as initial reference(s) for subsequent refinement. The
refinement block is concerned with the optimisation of reconstruction(s) from imaging data associated with each particle position.
Each of these ‘blocks’ is a world unto itself, and this abstraction is a gross oversimplification. Check the sidebar for more details!