Fig. 1.

The flowchart of AreTomo illustrates the major operations after a tilt series is loaded in the CPU memory. Each dash box represents an iterative procedure that involves two interdependent modules. The workflow contains both global and optional local alignments. The global alignment starts with the coarse alignment that is based on the pairwise correlation of each pair of the neighboring tilt images (Frank and McEwen, 1992). The subsequent refinement is based on the more accurate projection matching algorithm. The local alignment is performed on the globally aligned tilt series and measures and then corrects the residual local translations across the field of view for each tilt image.