Glossary

C

Cell type

A group of neurons with the same shape, position and connections, given a shared name such as T4a, LC4 or DNp01. One optic lobe of a male fly contains about 53,000 neurons classified into 732 types (Nern et al., 2025).

See: Neuron types

Central complex

A group of neuropils on the midline of the fly brain (the protocerebral bridge, fan-shaped body, ellipsoid body and noduli) that supports directed locomotion, sleep and navigation and keeps track of the fly’s heading (Hulse et al., 2021).

See: PFN neurons

Compound eye

An eye made of many ommatidia, each looking at a small part of the visual field. The browser previews on this site include a modeled compound-eye mosaic for inspection; the input the model receives is the separate 32-column retinal input.

See: Try it · Retinal input

Connectome

A map of the neurons of a nervous system and the synaptic connections between them. Fruit fly connectomes are reconstructed from electron microscopy: the hemibrain covers about 25,000 neurons of the central brain (Scheffer et al., 2020), FlyWire maps 139,255 neurons of a whole female brain (Dorkenwald et al., 2024), and the MaleCNS covers the brain and ventral nerve cord of a male.

See: Methods

D

Descending neuronDN

A neuron that carries signals from the brain through the neck to the ventral nerve cord. Complete connectomes count about 1,300 in the fruit fly, alongside about 1,700 to 1,900 ascending neurons that carry information the other way (Stürner et al., 2025).

See: Descending neurons · DNp01 (giant fiber) · DNa02

Drosophila melanogasterFruit fly · Common fruit fly · Vinegar fly

The common fruit fly, one of the most widely studied animals in genetics and neuroscience. A complete synapse-level wiring diagram of an adult female brain was published in 2024 (Dorkenwald et al., 2024). TheFlyBrain’s fly, Specimen 237, is a model of this species.

See: Specimen 237

E

Electron microscopy (EM)EM · FIB-SEM

Imaging with a beam of electrons instead of light, at a resolution high enough to see individual synapses. To build a connectome, a brain is imaged as a stack of very thin slices or milled layers, and every neuron is traced through the stack (Scheffer et al., 2020; Nern et al., 2025).

F

Fixed weights

Connection strengths that stay constant. The weights of TheFlyBrain’s model are the same in every experiment, so the model does not learn.

See: Methods

FlyEM

The project team at HHMI’s Janelia Research Campus that reconstructs fruit fly connectomes from electron microscopy, including the hemibrain (Scheffer et al., 2020) and the MaleCNS.

See: MaleCNS

FlyWire

A connectome of the whole brain of an adult female fruit fly: 139,255 neurons and about 50 million chemical synapses, reconstructed from electron microscopy, with annotations of cell types and predicted neurotransmitters (Dorkenwald et al., 2024).

H

Hemibrain

A 2020 connectome of the central region of a fruit fly brain: about 25,000 neurons and around 20 million connections, imaged in slices 8 nm thick (Scheffer et al., 2020).

K

Kenyon cellKC

An intrinsic neuron of the mushroom body. Kenyon cells respond sparsely to odors, and their synapses onto mushroom body output neurons are where dopamine is positioned to act during learning (Turner et al., 2008; Aso et al., 2014).

See: Kenyon cells

L

Lamina

The first neuropil of the optic lobe. It is built from cartridges, each receiving R1–R6 photoreceptor input and containing the lamina monopolar cells L1–L5 (Meinertzhagen and O'Neil, 1991).

See: Lamina monopolar cells

Leaky integrate-and-fire (LIF)LIF neuron

A simple spiking neuron model: each unit adds up its inputs, its voltage decays (leaks) back toward rest, and it fires a spike and resets when the voltage reaches a threshold. flybrain 0.1.0 uses LIF units with a common 100 ms membrane time constant and a 20 ms step, so it cannot represent rates above 50 spikes per second.

See: Model limitations

Lobula

A neuropil of the optic lobe that contains the dendrites of T5 motion detectors and of lobula columnar (LC) visual projection neurons, whose axons carry visual features to the central brain (Wu et al., 2016).

See: LC and LPLC neurons

Lobula plate

A neuropil of the optic lobe with four layers, one for each cardinal direction of motion, where the axons of the T4 and T5 subtypes terminate (Maisak et al., 2013).

See: T4 and T5 · LPLC2

Looming

The rapid expansion of an object’s image as it approaches on a collision course. In the fly, looming is detected by visual projection neurons such as LC4 and LPLC2, which drive the giant fiber escape neuron (Klapoetke et al., 2017; Ache et al., 2019).

See: LC4 · LPLC2 · DNp01 (giant fiber)

M

MaleCNSMale CNS connectome · MaleCNS v1.0

The connectome of the complete central nervous system of a male fruit fly, brain and ventral nerve cord, reconstructed from electron microscopy by FlyEM at HHMI Janelia and collaborators and released under CC BY 4.0. TheFlyBrain’s model uses the retained MaleCNS v1.0 graph of 166,700 neurons and 25,582,938 directed connections.

See: MaleCNS data (Janelia) · Specimen 237

Medulla

The second neuropil of the optic lobe, organized in columns and layers. R7 and R8 photoreceptors end here (Gao et al., 2008), and lamina signals are split into parallel channels, including the ON and OFF pathways that feed the T4 and T5 motion detectors (Takemura et al., 2013).

See: Mi and Tm neurons · R7 and R8

Micro-CTX-ray micro-computed tomography

X-ray micro-computed tomography: a scan that reconstructs an object’s 3D structure from X-ray images taken from many angles. The NeuroMechFly body model used for the fly is derived from micro-CT scans of a female fruit fly.

See: NeuroMechFly

Motor neuronMotoneuron · MN

A neuron whose axon ends on a muscle and makes it contract. About 50 motor neurons operate each fruit fly leg (Azevedo et al., 2020).

See: Leg motor neurons

Mushroom body

A paired brain structure for associative learning and memory, formed on each side by the parallel axons of about 2,000 Kenyon cells and divided into 15 compartments by output and dopaminergic neurons (Aso et al., 2014).

See: Kenyon cells · PAM dopaminergic neurons

N

NeuroMechFlyNeuroMechFly v2

An open neuromechanical model of the adult fruit fly body; version 2 adds vision, olfaction, ascending motor feedback and complex terrain (Wang-Chen et al., 2024). The fly on this site uses NeuroMechFly v2 body assets with 69 articulated segments. Its body and the MaleCNS nervous system come from different specimens and are not anatomically registered.

See: Specimen 237 · Methods and credits

NeuronNerve cell

A cell that carries signals in the nervous system. A neuron receives input on its dendrites and passes signals along its axon to other cells through synapses. Most insect neurons are unipolar: a single neurite leaves the cell body and branches into dendrites and axon.

See: Neuron types

O

OmmatidiumOmmatidia · Unit eye

One of the many unit eyes that make up the compound eye. Each fruit fly ommatidium has its own lens and eight photoreceptors, R1 to R8 (Meinertzhagen and O'Neil, 1991).

See: R1–R6 · R7 and R8

ON and OFF pathways

Parallel visual channels for brightness increments (ON) and decrements (OFF). In the fly they begin with lamina neurons L1 (ON) and L2 (OFF) and end in the T4 (ON) and T5 (OFF) motion detectors (Joesch et al., 2010; Maisak et al., 2013).

See: L1–L5 · T4 and T5

Optic flow

The pattern of motion across the eyes produced by an animal’s own movement, such as the wide-field rotation seen when a fly turns. In the fly, local motion is computed by T4 and T5 and integrated by wide-field motion-sensitive neurons of the lobula plate (Maisak et al., 2013).

See: T4 and T5

Optic lobe

The visual part of the fly brain on each side, behind the compound eye. Its neuropils are the lamina, medulla, lobula and lobula plate. One optic lobe of a male fly contains about 53,000 neurons (Nern et al., 2025).

See: Lamina · Medulla · Lobula · Lobula plate

P

Photoreceptor

A light-sensing cell. Each fruit fly ommatidium has six outer photoreceptors (R1–R6), used mainly for motion vision, and two inner ones (R7 and R8), which provide color vision (Gao et al., 2008; Wardill et al., 2012).

See: R1–R6 · R7 and R8

R

Retinal input (32 columns)Retina · 32-column retina

The visual input of TheFlyBrain’s model. Each scene is rendered from the fly’s head, averaged vertically into 32 luminance columns across the visual field, and delivered to the model’s photoreceptors by estimated azimuth. It carries no color or vertical structure, is not a model of compound-eye optics, and display settings never change it.

See: Methods · R1–R6

S

Skeleton reconstructionNeuron skeleton

A simplified representation of a reconstructed neuron as a tree of connected points that follows its branches. The 3D views on this site draw downsampled skeletons of 626 MaleCNS neurons.

See: Explore the nervous system

SomaCell body

The cell body of a neuron, which contains the nucleus. In insects the somata lie in a rind, the cortex, around the neuropils, connected to the neuron’s branches by a single neurite. The faint dots in the site’s 3D views mark a sample of MaleCNS soma positions.

Spiking neural networkSpiking neuron model · flybrain

A model in which each neuron produces discrete spikes when its membrane voltage crosses a threshold, and the spikes reach other neurons through weighted connections. TheFlyBrain’s workstation runs the MaleCNS graph as such a network with flybrain 0.1.0, an open-source Python package (MIT License).

See: Methods

Synapse

A junction where one neuron passes a signal to another. At a chemical synapse the sending cell releases a neurotransmitter; at an electrical synapse current flows directly between cells through gap junctions. Electron-microscopy connectomes record the chemical synapses between neurons (Dorkenwald et al., 2024).

Synaptic plasticityPlasticity

An activity-dependent change in the strength of a synapse, the cellular basis of learning. In the mushroom body, dopaminergic neurons are positioned to modify the synapses from Kenyon cells onto output neurons (Aso et al., 2014). TheFlyBrain’s model has no plasticity.

See: Kenyon cells · PAM dopaminergic neurons

V

Ventral nerve cord (VNC)VNC · Nerve cord

The part of the fly’s central nervous system in the thorax, its counterpart of the spinal cord, which contains the circuits that sense and move the legs and wings. The ventral nerve cord of an adult female contains roughly 14,600 neuronal cell bodies and 45 million synapses (Azevedo et al., 2024).

See: Leg motor neurons

Visual projection neuronVPN · Optic glomerulus

A neuron that carries visual information from the optic lobe to the central brain. Each lobula columnar (LC) type sends its axons to its own compact target region, an optic glomerulus (Wu et al., 2016).

See: LC and LPLC neurons