Neuronal coordinates of C.elegans
The Worm Atlas you cited is NOT just a "model." The neuronal cell coordinates were determined from an actual 3-D reconstruction of a worm based on serial thin section electron micrographs.  The serial sections were manually digitized to permit annotation and analysis using computer graphics. The annotation (over a period of years) established the synaptic connectivity, published by John White et al. in 1986 in the Proceedings of the Royal Society of London.