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FlyEM / Hemibrain

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FlyEM / Hemibrain
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FlyEM / Hemibrain
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The hemibrain connectome includes many of the brain areas that scientists are most interested in studying, such as circuits that control learning, memory, and key fly behaviors.

The hemibrain connectome is the largest synaptic-level connectome ever reconstructed. It covers a large portion of the central fly brain, including the mushroom body and central complex circuits critical for associative learning and fly navigation. Clock neuron circuity included in the volume could also provide insights on mechanisms underlying sleep. Furthermore, given available light microscopy image data and previous partial connectome reconstruction in the optic lobe, we also identified most optic lobe neurons entering the cental brain regions enabling analysis of downstream visual processing.

This connectome reconstruction contains around 25,000 neurons, which can be grouped into thousands of distinct cell types spanning several brain regions. This connectome required advances in imaging, segmentation (by the Connectomics Group at Google), and proofreading and analysis software.

Getting started


The FlyEM team has developed free tools to sort through the connectome data, including NeuPrint. Using this tool, scientists can search for particular cell types and identify connection pathways between specific areas or neurons.

Resources and relevant technologies

Biological exploration & analysis

Programming and data access


Videos of hemibrain circuitry

Neuroscientists are already using connectome data to understand the mechanistic underpinnings of fly behavior. The circuitry shown here is from the fly’s central complex, a region that controls navigation.


To image the Drosophila hemibrain, researchers precisely cut the fly brain into relatively thick slabs using a hot knife.  Each slab is then imaged using focused ion beam and scanning electron microscopy (FIB-SEM) to generate data with nanometer isotropic resolution. Afterwards, images from different sections were carefully stitched together. The goal: To create an image volume with as little aberration along the boundaries as possible, to make tracing the paths of neurons through the brain possible.


Researchers have identified more than 4,000 distinct types of neurons in the Drosophila hemibrain. Here are a few of them.


Completing the hemibrain connectome required optimizing every part of the process, from the microscopes that imaged the brain to the algorithms that automatically traced neurons through the dataset. This video gives an overview of the endeavor.