Fig. 2.

Extraction of polyhedral graph from cryo-EM reconstructions: a Upper level cross-sectional slice showing an MC with boundary partially visible due to poorer resolution. The scale bar is 50 nm. b Hand-drawn segmentation showing interior (deep green), exterior (yellow). Light green indicates a conservatively drawn region of uncertainty (caused by poor resolution) in which we suspect the object boundary lies. This region of uncertainty is used to constrain the 3-d reconstruction. c Stacked hand drawn boundaries from slices along the z-axis. Note that boundary information is completely missing for slices above and below this stack. d Volume rendering of regularized least squares reconstruction of object using data from stack in (b). Note missing wedge on right hand side. e Volume rendering of regularized least squares reconstruction of object using data from stacks of slices along x, y and z-axis. f Ball and stick diagram of polyhedral graph (PG) for object in (e), drawn using Chimera. Blue balls are observed vertices. Red lines are completed edges. Yellow lines are incomplete edges. Green balls are ends of incomplete edges