Neuronal wiring diagram of an adult brain

Although rudimentary nervous systems existed in more ancient animals, brains evolved around half a billion years ago, and are essential for the generation of sophisticated behaviours. It is widely accepted that dividing a brain into regions is helpful for understanding brain function, but questions remain on the utility of finer-grain information about connectivity. In fact, efforts to construct wiring diagrams at the level of neurons and synapses have been controversial. Scepticism has flourished largely owing to a lack of technologies that could reconstruct such wiring diagrams, so obtaining such diagrams has remained hypothetical. The situation began to change in the 2000s owing to the efforts of a small community of researchers. Here we present a neuronal wiring diagram of a whole adult brain and, here and in the accompanying studies, we analyse its connectivity to highlight the utility of this endeavour.

Although small, the brain of D. melanogaster contains 10⁵ neurons and 10⁸ synapses that enable a fly to see, smell, hear, walk and fly. Flies engage in dynamic social interactions, navigate over distances and form long-term memories. Portions of fly brains have been reconstructed from electron microscopy images, which have sufficient resolution to reveal the fine branches of neurons and the synapses that connect them. The resulting wiring diagrams of neural circuits have provided crucial insights into how the brain generates social, memory-related or navigation behaviours. Wiring diagrams of other fly brain regions have been mapped and related to visual, auditory and olfactory functions. The circuit organization revealed by these wiring diagrams show similarities to mammalian brains.

These wiring diagrams and many others from mammals have been derived from pieces of brain. However, recordings of Drosophila neural activity have revealed nearly brain-wide encoding of sensory and motor variables. These studies and others in vertebrates highlight that understanding how the brain processes sensory information or drives behaviour will require understanding global information flow at the scale of the entire brain.

Until now, the closest antecedent to a wiring diagram of the whole brain has been the reconstruction of a fly ‘hemibrain’, a pioneering resource that has already become indispensable to Drosophila researchers. It is estimated to contain around 20,000 neurons that are ‘uncropped’—that is, minimally truncated by the borders of the imaged volume, and 14 million synapses between them. Our reconstruction of an entire adult brain contains 139,255 neurons (Fig. 1a and Supplementary Video 1) and 54.5 million synapses between these neurons. To aid exploration and analysis, this connectome has been densely annotated by the FlyWire Consortium. In our companion paper, Schlegel et al. provide a curated brain-wide hierarchy of annotations including more than 8,400 distinct cell types, completing the description of this resource (and should therefore preferably be cited alongside this paper; https://codex.flywire.ai/about_flywire). These and many other data products (Fig. 1b and Supplementary Fig. 1) are available for download, programmatic access and interactive browsing and have been made interoperable with other fly data resources through a growing ecosystem of software tools (Fig. 1c). The primary portal to the data is the FlyWire Connectome Data Explorer (Codex; https://codex.flywire.ai/), which makes the information visualizable and queryable.

The wiring diagram from our whole-brain reconstruction is sufficiently complete to be designated a ‘connectome’ (defined in Discussion). It represents substantial progress over neuronal reconstructions of Caenorhabditis elegans (300 neurons, 10⁴ synapses) and the 1st instar larva of Drosophila (3,000 neurons, 5 × 10⁵ synapses). Our connectome advances beyond the hemibrain in several ways. For example, it includes the suboesophageal zone (SEZ) of the central brain, which is important for diverse functions such as gustation and mechanosensation, and contains many of the processes of neurons that descend from the brain to the ventral nerve cord to drive motor behaviours. Additionally, it includes annotations for descending and ascending neurons for many sexually dimorphic neurons (analysed by Deutsch et al. (manuscript in preparation); available at https://codex.flywire.ai) and an entire optic lobe. Our reconstruction of both optic lobes goes far beyond existing maps of columnar visual circuitry. Connections between the optic lobes and central brain are included, as explored by refs.. Also included are neurons that extend into the brain through the nerves and neck connective, which are essential for tracing sensorimotor pathways, as illustrated here and in the accompanying studies.

Our reconstruction utilized image acquisition and analysis techniques that are distinct from those used for the hemibrain (Methods and Discussion). However, we have built directly on the hemibrain in an important way. Schlegel et al. used the cell types proposed for the hemibrain as a starting point for cell typing neurons in the central brain in FlyWire. This approach was enabled by a growing ecosystem of software tools serving interoperability between different fly data sources (Fig. 1c). Additional annotations in the SEZ and optic lobes, which are largely absent from the hemibrain, were contributed by Drosophila research groups in the FlyWire Consortium as well as citizen scientists, and are described in more detail here and in the accompanying papers. Synapse predictions and estimates of neurotransmitter identities were also contributed by the community.

After matching, Schlegel et al. also compared our wiring diagram with the hemibrain where they overlap and showed that cell-type counts and strong connections were largely in agreement. This means that the combined effects of natural variability across individuals and ‘noise’ due to imperfect reconstruction tend to be modest, so our wiring diagram of a single brain should be useful for studying any wild-type Drosophila melanogaster individual. However, there are known differences between the brains of male and female flies. In addition, principal neurons of the mushroom body, a brain structure required for olfactory learning and memory, show high variability. Some mushroom body connectivity patterns have even been found to be near random, although deviations from randomness have since been identified. In short, Drosophila wiring diagrams are useful because of their stereotypy, yet also open the door to studies of connectome variation.

In addition to describing the FlyWire brain resource, this Article also presents analyses that illustrate how the data products can be used. Additional whole-brain network analyses are provided by Lin et al. and Pospisil et al.. From the connectome, we derive a projectome, a reduced map of projections between 78 fly brain regions known as neuropils (Fig. 1d, Extended Data Fig. 1 and Supplementary Video 2). We trace synaptic pathways and analyse information flow from the inputs to the outputs of the brain, across both hemispheres, and between the central brain and the optic lobes. In particular, the organization of excitation and inhibition in pathways from photoreceptors in the ocelli to descending motor neurons immediately suggests hypotheses about circuit mechanisms of behaviour.