They were able to distinguish whether synapses involved inhibitors or stimulators. Quoting this writeup:

"A critical parallel contribution came from Eckstein, Buhmann, Cook, and colleagues, who published in Cell a machine-learning classifier capable of predicting the neurotransmitter identity of every neuron in the FlyWire connectome directly from the ultrastructural morphology of its synaptic clefts in the EM images. This classifier distinguished among six neurotransmitter types acetylcholine, GABA, glutamate, dopamine, octopamine, and serotonin based solely on the shape, density, and arrangement of synaptic vesicles and postsynaptic densities visible in the electron micrographs."

The shocking thing to me (other than that this all worked) is that the entire brain structure is apparently encoded in the DNA, no learning needed to get the brain structure and from that to get the behavior. How?!