Ground truth annotation workflow for ER and Golgi apparatus. (A and B) Example of graph-cut assisted segmentation used to generate the ground truth annotation for ER (A) or Golgi apparatus (B) in Cell 1 HEK293A prepared by chemical fixation and visualized with ∼5 nm isotropic resolution. Coarse annotations for background (lines, solid areas in pink) and object (dotted lines in yellow) drawn in the indicated broadly spaced planes of the stack were used as seeds to generate the ground truth annotations with the graph-cut assisted segmentation program.