Neuronal wiring diagram of an adult brain

For mammals, tracer injection studies have mapped the axonal projections between brain regions of mouse and macaque. In the fly, large numbers of light microscopy reconstructions of single neurons have been aggregated to map projections between brain regions. Such maps have been called projectomes or mesoscale connectomes. In such techniques, the sampling of axons is difficult to control, and therefore accurate quantification of projection strength is challenging.

Here we computed a projectome from a synapse-level connectome (Fig. 4a and Extended Data Fig. 5). The interior of the fly brain has been subdivided into hierarchical neuropil regions (Fig. 1 and Extended Data Fig. 1). Our fly projectome is defined as a map of projections between these neuropil regions. Because cell bodies are spatially separated from neuropils, a fly neuron cannot typically be assigned to a single brain region. This is unlike the situation for a mammalian neuron, which is conventionally assigned to the region containing its cell body. A typical fly neuron belongs to multiple neuropils.

The projectome is a neuropil–neuropil matrix, and is computed as follows. Each intrinsic neuron contributes to the projections between neuropils where it has presynaptic and postsynaptic sites. We weighted neuron projections by the product of the respective number of synapses and normalized the result for every neuron such that the neuropil–neuropil matrix sums to the total number of intrinsic neurons. Each column corresponds to all the neurons projecting to a neuropil and each row corresponds to to all neurons projecting out of it (Fig. 4b). Each square then represents the summed fractional weight of all neurons projecting between two neuropils (Fig. 4c,d). We added afferent and efferent neurons to the matrix by calculating the sum of the weighted neuron projections per superclass to and from all neuropils, respectively.

Whereas each neuropil is connected to many others, most neurons have synaptic sites in only a few neuropils (Fig. 4e). The largest weights in the projectome tend to be internal to individual neuropils, such as within the medulla or within the fan-shaped body. The largest inter-neuropil projections overall are lobula to medulla, whereas within the central brain the largest inter-neuropil projections are mushroom body, medial lobe to mushroom body, calyx.

We repeated this process to construct projectomes for each fast neurotransmitter type (Extended Data Fig. 5). Some neuropil–neuropil connections exist strongly for one neurotransmitter but not others. For example, the neuropils making up the central complex (fan-shaped body, ellipsoid body, protocerebral bridge and noduli) and the mushroom body (calyx, pendunculus, vertical lobe and medial lobe) are largely linked by excitatory connections.

We observed a strong symmetry between projections in the left and right hemisphere as well as with the central neuropils located on the midline (Extended Data Fig. 6a,b); this highlights the strong similarity between the two sides of the brain. We observed that contralateral projections (projections from one side of the brain to the other) were generally weaker than projections to the same or ipsilateral neuropil (Extended Data Fig. 6c). The strongest contralateral projections are between left and right superior protocerebrum, followed by left and right anterior ventrolateral protocerebrum. Of note, projection weights were not strongly correlated to inter-neuropil distance. Although the strongest projections are often between nearby neuropils, there are also many nearby neuropils that do not share strong connections (Extended Data Fig. 6d).

The SEZ (Fig. 4f) is the ventral portion of the central brain, and has been shown to contribute to a variety of behaviours. It is almost entirely unrepresented in the hemibrain reconstruction, and is only partially reconstructed in the larval brain. The five neuropils in the SEZ (left and right AMMC, GNG, SAD and PRW; Fig. 4f; breakdown by neuropil in Supplementary Figs. 4 and 5) amount to 17.8% of central brain neuropil volume (0.0018 mm³ out of 0.0103 mm³); they contain afferents mostly from non-visual sensory neurons (mechanosensory and taste) and ascending neurons, as well as a large number of efferents (motor, endocrine and descending neurons; descending neurons receive on average 52% of their inputs in one of the five SEZ neuropils). The SEZ is thus important for information flow to and from the brain. Judging from the projectome (Fig. 4a), the SEZ neuropils interact with almost all parts of the brain. Notable exceptions are the central complex (ellipsoid body, fan-shaped body, protocerebral bridge and noduli) and the mushroom body, suggesting less crosstalk between those circuits and neurons in the SEZ (explored in more detail in Fig. 6; see also Pospisil et al.).