Mapping the complete male fruit fly brain

Steps toward mapping a full fruit fly brain

Brain mapping, or connectomics, begins with sectioning a brain into millions of thin slices, taking an image of each section, and using computers and AI to stitch the images together. Our researchers build systems that leverage AI to turn flat electron microscope images into 3D reconstructions, using an evolving suite of techniques to generate accurate neural shapes.

Our AI connectomics tools include flood-filling networks, which use convolutional neural networks to start at a single pixel and identify all other pixels that are part of the same object. In 2019, our Connectomics team released an initial, fully-automated reconstruction of a female fruit fly brain. By 2020, our team and collaborators released a human-verified map of half a female fruit fly brain with 25,000 neurons and 21 million connections, a record at the time. Meanwhile, the team was already working on the full, verified brain map for a male fruit fly, which is now complete.

These methods continue to improve. A recent effort incorporated synthetic neurons into the training data, successfully improving the speed and accuracy of our state-of-the-art reconstruction system, PATHFINDER. We are also helping to develop new techniques for labeling and annotating specific types of neurons. Currently, mapping the fruit fly brain requires years of human effort just to verify and annotate the neural shapes. By reducing this need for manual error correction, research groups can tackle even larger brain mapping projects within reasonable budgets and timelines.