I worked on the Human Connectome Project.

If they freeze the vesicles that deliver transmitters and make them analyzable, you've got all the information you need. In terms of a modern ANN, it's the connections (axons) and the weights (transmitters/receptors in tandem).

That said, this article doesn't get to the point in the free section. How are they collecting the information? Slicing is inherently destructive. Someone's got to manufacture an entirely novel imaging modality. Perhaps they could scan millimeters ahead of the slice at a resolution high enough to image receptors. Not possible currently.

It is my understanding that for the animals where we have a simulation of the full connectome the behavior you see approximates the real behavior reasonably well, so maybe the jury is still out as to whether it is sufficient or not.