Figure 1

Slice extraction and nuclear definition. a. An x,y plane through C. elegans volume data at the ~350 cell stage. b. the corresponding slice through the 3D DoG filtered volume. c. Slices are segmented by casting out rays in search of a zero crossing. The 2D intensity maxima where rays originate are marked as black dots. Final end points of search rays are marked as blue dots. These points define a polygonal slice; multiple slices can be assembled together to yield a 3D nuclear boundary. d. Nuclear shape definition. The position, intensity, and size of each slice that might be part of a nucleus are measured relative to the nuclear center, and also relative to the closest slice between the possible member and the nuclear center. These measurements make up the 7D vector that represents a slice and nucleus center pairing. Actual nuclear extraction starts from the center and in turn considers the likelihood of each slice as an endpoint for the nucleus.