Second complete map of a fruit fly brain completed

All that processing is dictated by which neurons have connections to others. For example, the visual system does some basic recognition of its own before passing the results to the brain’s visual processing centers. If those centers detect something like text, they can use connections to the language centers to interpret it, and so on. To understand how a brain works, then, we need a catalog of the connections in the brain, since those dictate how information flows through its various systems. That catalog is a connectome. In practical terms, a connectome is the list of every neuron in a brain, including its location in three-dimensional space, and the connections (termed synapses) it forms with other neurons. That’s more complicated than it may sound. Each neuron can form multiple, branched processes called axons, allowing it to form hundreds of connections to other neurons. So while the nervous system of the fruit fly consists of only roughly 150,000 neurons, and the brain contains only a fraction of those, the new work discovered over 300 million synaptic connections in the fly brain. So how do you go about mapping something like that? Gerry Rubin, a senior group leader at the Janelia Research Campus and one of the senior authors on the new paper, described how things have changed considerably based on the complexity of the system. “I was a graduate student at the [UK’s Laboratory of Molecular Biology]… and when I got there in 71, they already bought this giant computer, and they had the idea that they were going to use machine vision and computers to assemble the C. elegans connectome,” Rubin said. C. elegans is a small, transparent worm with just over 300 neurons and would seem to be a tractable system. “It took them about two years to realize that the computers were nowhere near powerful enough,” Rubin said, “and so they went with printing everything out on photographic prints and colored magic markers and circling neurons and tracing it by hand.” Still, other models are used to recognize synapses and classify the type of synapse once it’s spotted. These models can be fine-tuned using different levels of sensitivity, or “greediness”—basically, adjusting the probability that they’ll call something a synapse. And here, feedback from human proofreaders plays a major role. “This has to be tuned by going back and forth between the proofreaders and Mikhail to say, ‘Oh, give us a version where you were less greedy because it’s harder to disassemble than it is to assemble,’” Rubin said. “So it’s an iterative process between the humans giving feedback and the algorithms getting tuned.” All of this took roughly four years to go from an intact fly brain to the complete connectome. But Rubin said the techniques the team developed along the way, along with the growing sophistication of the software, will hopefully be critical as connectomics work moves up the complexity scale. “Our view is we did Drosophila with a team of 50 people,” Rubin said. “The hope is, by the time someone does a mouse, they’ll also need a team of 50 people, even though there are a thousand times more neurons in there. The people will never go away, but the people will not need to scale with the number of neurons, which would be economically not feasible.” Managing this complexity is also what drew Google to the challenge. “The reason I think Google and we were interested in this is because this is this type of grand challenge that just cannot be done in any other way,” Januszewski said. “We knew we need AI for this. This cannot be solved by having more humans or by any other technology. And it’s important.” Due to the extensive history of research on Drosophila, we already knew a great deal about the fly nervous system, including the functional regions of the fly brain and an assortment of individual neurons that had been identified by a combination of function and/or gene activity. But it was at best a partial picture, one that we can use the connectome to fill out in more detail. Combined with the completion of the connectome of a female fly that was completed by university-based researchers earlier this year, we’re able to understand a bit more about how sex determination feeds into specific brain differences. This builds on an extensive genetic understanding of how sex determination works in flies (my thesis work provided a very tiny contribution here), which has identified two genes, doublesex (dsx) and fruitless (fru), as being factors in converting the number of X and Y chromosomes into overt differences in, among other things, behavior. So, one of the things the researchers were able to do is look at what neurons were different between males and females, and how many of those differences could be directly ascribed to the activity of these two genes. And as with so many things in biology, the basic numbers look simple but the details are fairly complex. The researchers identified 289 male-specific neurons, 71 female-specific ones, and 138 that were present in both sexes but formed a different shape and connections in males and females. Their relationship to the genes mentioned above was not always direct. Ninety percent of the male-specific neurons were making dsx and fru, but that leaves 10 percent that weren’t. Rubin suggested these had likely picked up a sex-specific identity by interactions with those that were. Rubin also suggested it’s having a big impact on theoretical neuroscience. “Before this, most neuro theorists were very much like, ‘How could a brain work?’” he said. “And they didn’t have a constraint. Once they had the connectome, they could say, ‘The brain does this and here’s the wiring diagram. How can this wiring diagram allow this function?’ So this has been a major. I’d say this is the biggest change in having the connectome.” Other work will depend on whether completing connectomes follows the trajectory seen in genomics, where the cost drops precipitously as techniques are refined and further automated. One of this work’s most intriguing findings is that a specific neuron seen in the female connectome was absent from one of the two hemispheres of the male fly, presumably due to a developmental glitch. With only two connectomes complete, it’s impossible to get a good sense of how common this sort of variability is. The same applies to subtler differences in the trajectories taken and connections made by individual neurons. To say anything meaningful about this kind of variability with statistical confidence, we’ll need dozens of examples. That means we’ll also need to make the process much faster than the four years it took to go from dissecting a fly brain to the final connectome. Cell, 2026. DOI: 10.1016/j.cell.2026.08.015 (About DOIs).