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How to Pick a Fly’s Brain

Janelle Weaver, Ph.D.

Recent technical breakthroughs have led to new insights into how neural circuits in the fly brain process visual motion. Learn more...

Most of the neurons in the fly brain are dedicated to vision, but despite decades of research, the neural computations involved in perceiving motion are not well understood. The anatomy of these neural circuits has remained mysterious due to a lack of detailed synaptic connection maps, or connectomes. Meanwhile, insights into the function of cells in these circuits have been limited because some visual neurons in the fly brain are too small to be recorded in electrophysiological studies. Two studies published in Nature have made significant progress toward overcoming these technical hurdles, revealing new insights into the neural basis of motion perception in fruit flies.

Connectome reconstruction using serial-section electron microscopy

In the first study, researchers developed a semi-automated, high-throughput pipeline using electron microscopy to reconstruct the connectome of a small, motion-processing circuit in the optic lobe of the fruit fly brain (1). “This is probably the most sophisticated electron microscopical study so far attempted, allowing for the reconstruction of every neuron and perfect serial sections showing every synapse,” said Nicholas Strausfeld of the University of Arizona, who was not involved in the study.

First, the researchers cut the optic lobe into a few thousand sections and imaged them using transmission electron microscopy. They then used automated image analysis techniques to align and assemble the sections into a three-dimensional stack and delineate nearly 400 individual neurons. By comparing the shapes of the reconstructed neurons to those reported in previous light microscopy studies, they classified most of these neurons into 56 different cell types. This step would have been impossible had they tried to determine cellular identities one electron micrograph at a time.

The most difficult part of the protocol was determining how these neurons were connected in the circuit. This manual step required the researchers to collectively spend more than 14,000 hours reading electron micrographs and identifying about 9,000 synaptic connections between neurons. “This is a real tour de force, but clearly image analytic software will need to improve so that this part of brain connectomics can also become automated,” wrote Cole Gilbert of Cornell University in a Current Biology article about the new studies (2).

As long as the research is so time-consuming, it will remain limited in scope. “Impressive as the studies are, this is a drop in the bucket compared to how the entire fly brain is working,” said Loren Looger of the Janelia Farm Research Campus. “The field needs five to ten more orders of magnitude improvement in the acquisition and interpretation of such datasets to even plausibly live up to the lofty rhetoric of the BRAIN Initiative and its stated aim of figuring out how the brain works.”

The second study focused on the functional properties of the motion circuit (3). Two types of neurons in this circuit—T4 and T5 cells—have long been thought to play an important role in motion detection. Because these cells are so small, it has been difficult to obtain electrical recordings from them. To overcome this hurdle, Alexander Borst of the Max Planck Institute of Neurobiology and his team took advantage of novel genetic methods available in the fruit fly to optically record the activity of T4 and T5 cells using two-photon fluorescence microscopy. Specifically, they used a genetically encoded calcium indicator known as GCaMP5—a more sensitive tool for detecting neural activity recently developed by Looger and his collaborators (4).

When the researchers exposed flies to moving visual patterns, they found that T4 and T5 cells responded to specific directions of motion. T4 cells responded to visual motion of light, but not dark, edges; the reverse was true for T5 cells. This finding confirms the existence of two separate “ON” and “OFF” motion pathways, settling a long-standing controversy in the field. “That is exactly how the motion-sensing units in our retina are organized,” Borst said. “Given the many hundreds of millions of years that vertebrates and insects are separated in evolution, that tells us that this is a very important principle of how the visual world is processed by the early nervous system.”


1. Takemura SY, Bharioke A, Lu Z, Nern A, Vitaladevuni S, Rivlin PK, Katz WT, Olbris DJ, Plaza SM, Winston P, Zhao T, Horne JA, Fetter RD, Takemura S, Blazek K, Chang LA, Ogundeyi O, Saunders MA, Shapiro V, Sigmund C, Rubin GM, Scheffer LK, Meinertzhagen IA, Chklovskii DB. 2013. A visual motion detection circuit suggested by Drosophila connectomics. Nature. 500(7461):175-81. doi: 10.1038/nature12450.

2. Gilbert C. 2013. Brain connectivity: revealing the fly visual motion circuit. Curr Biol. 23(18):R851-3. doi: 10.1016/j.cub.2013.08.018.

3. Maisak MS, Haag J, Ammer G, Serbe E, Meier M, Leonhardt A, Schilling T, Bahl A, Rubin GM, Nern A, Dickson BJ, Reiff DF, Hopp E, Borst A. 2013. A directional tuning map of Drosophila elementary motion detectors. Nature. 500(7461):212-6. doi: 10.1038/nature12320.

4. Akerboom J, Chen TW, Wardill TJ, Tian L, Marvin JS, Mutlu S, Calderón NC, Esposti F, Borghuis BG, Sun XR, Gordus A, Orger MB, Portugues R, Engert F, Macklin JJ, Filosa A, Aggarwal A, Kerr RA, Takagi R, Kracun S, Shigetomi E, Khakh BS, Baier H, Lagnado L, Wang SS, Bargmann CI, Kimmel BE, Jayaraman V, Svoboda K, Kim DS, Schreiter ER, Looger LL. 2012. Optimization of a GCaMP calcium indicator for neural activity imaging. J Neurosci. 32(40):13819-40. doi: 10.1523/JNEUROSCI.2601-12.2012.