Workflow
Acquire a tilt series with tom_tilt_series.
Result: tilt series

Sort the acquired tilt series according to their tilt angle with tom_processdirgui
Result: sorted tilt series

Align the sorted tilt series with tom_setmark
Result: markerfile.em

Make a reconstruction with tom_Rec3dGUI. Just load the markerfile and the projections. The file includes the alignment parameters and the path of the tilt series.
Result: volume in .em format

Visualize the volume with tom_volxyz

