flywire — FlyWire whole adult fly brain (2024)

Description

The connectome of the entire brain of an adult female fruit fly Drosophila melanogaster, reconstructed by the FlyWire Consortium from the serial-section transmission electron microscopy volume "Full Adult Fly Brain" (FAFB), with automated segmentation and synapse detection followed by extensive manual proofreading by a community of researchers and citizen scientists. This is the public release v783 of the data set. Nodes are the 139,255 proofread neurons, and a directed edge $(i, j)$ indicates chemical synapses from neuron $i$ (presynaptic) to neuron $j$ (postsynaptic) within a given brain region (neuropil).

Synapses were detected automatically, and only those with a cleft score of at least 50 are included, as in the authors' analyses. As in the fly_hemibrain entry, the connections between a pair of neurons are split according to the neuropil where the synapses reside, so that the same pair of neurons may be connected by several parallel edges, one per neuropil. There are three networks:

min5: following the authors, who consider a pair of neurons to be connected if there are at least five synapses between them (which makes false-positive connections very unlikely), only the pairs of neurons with at least five synapses in total (summed over all neuropils) are included: these are 2,700,513 of the 15,091,983 connected pairs, carrying 34.2 million of the 54.5 million synapses between proofread neurons (the weight of an individual edge, in one neuropil, may be smaller than five).
all: all connections, without threshold on the number of synapses.
synapses_all: the same as all, but aggregated here from the table of all the individual synapses released with the data (130,054,535 synapses, with their positions, cleft scores and neurotransmitter predictions), instead of the table of connections between proofread neurons. This table is not unthresholded: the synapses with a cleft score below the threshold were not released (all the scores in the table are above 50), so that it contains the same synapses, and the network differs from all only in details. Of these synapses, the 54,492,970 between two proofread neurons are included, while the 75,561,565 that involve at least one segment that is not a proofread neuron (e.g. fragments that could not be attached to a neuron) are left out. The network has 16,848,018 edges, 21 more than all (in ME_R, with 48 synapses in total), which are missing from the table of connections. The synapses without a neuropil (marked None in the table) are assigned to UNASGD, as in the other networks. The neurotransmitter probabilities are the averages of the predictions for the individual synapses; they differ from those of the other networks for the outgoing connections of the Kenyon cells (whose predictions are mostly dopamine), for which the table of connections gives an acetylcholine probability of one. The predictions are missing for 5,347 synapses, which are left out of the averages (they are NaN for the 370 edges where they are missing for all the synapses). The edges also carry the averages of the cleft and connection scores of the synapses; the positions of the individual synapses are not included.

The neuron annotations are those published with the paper of Schlegel et al. (Supplementary Data 1), with cell types matched to the hemibrain and new ones; all networks have the same nodes, so that in min5 the neurons that make no connection with at least five synapses are isolated nodes.

The networks have the following properties:

(Node) root_id: the neuron's identifier in the FlyWire data set (root ID of the v783 release).
(Node) flow: whether the neuron is intrinsic to the brain, afferent or efferent.
(Node) super_class: the coarsest neuron classification (e.g. central, optic, sensory, visual_projection, ascending, descending, motor, endocrine).
(Node) cell_class, cell_sub_class: finer neuron classes (e.g. Kenyon_Cell, ME>LO); empty if not assigned.
(Node) cell_type: the cell type of the neuron, either new or a refinement of a hemibrain type; empty if not assigned.
(Node) hemibrain_type: the hemibrain cell type(s) matched to the neuron (see the fly_hemibrain entry); empty if not assigned.
(Node) hemilineage: the developmental hemilineage of the neuron (Ito-Lee nomenclature); empty if not assigned.
(Node) side: the side of the brain where the neuron's soma (or, for sensory neurons, its entry point) is located (left, right, center).
(Node) nerve: the nerve through which the neuron enters or exits the brain, for afferent and efferent neurons; empty otherwise.
(Node) top_nt: the neurotransmitter predicted for the neuron from its synapses (acetylcholine, glutamate, gaba, dopamine, serotonin, octopamine); empty if not assigned.
(Node) top_nt_conf: the confidence of the neurotransmitter prediction (NaN if not assigned).
(Edge) neuropil (edges): the neuropil in which the synapses of the connection are located (e.g. ME_L for the medulla of the left hemisphere; UNASGD if unassigned).
(Edge) weight (edges): the number of synapses from $i$ to $j$ in that neuropil.
(Edge) gaba, ach, glut, oct, ser, da (edges): the probabilities that the synapses of the connection release GABA, acetylcholine, glutamate, octopamine, serotonin or dopamine, predicted from the electron microscopy images and averaged over the synapses.
(Edge) cleft_score, connection_score (edges, synapses_all only): the cleft score (from the synaptic cleft segmentation of Heinrich et al., used for the threshold) and the connection score (from the synaptic partner detection of Buhmann et al.) of the synapses, averaged over the synapses; higher is better.

Tags

Biological Connectome Weighted Multigraph Metadata

Added

2026-10-27

Citation

S. Dorkenwald et al., "Neuronal wiring diagram of an adult brain." Nature 634, 124-138 (2024) 10.1038/s41586-024-07558-y Sci-Hub
P. Schlegel et al., "Whole-brain annotation and multi-connectome cell typing of Drosophila." Nature 634, 139-152 (2024) 10.1038/s41586-024-07686-5 Sci-Hub
J. Buhmann et al., "Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set." Nature Methods 18, 771-774 (2021) 10.1038/s41592-021-01183-7 Sci-Hub
L. Heinrich, J. Funke, C. Pape, J. Nunez-Iglesias, S. Saalfeld, "Synaptic cleft segmentation in non-isotropic volume electron microscopy of the complete Drosophila brain." Medical Image Computing and Computer Assisted Intervention (MICCAI 2018), 317-325 (2018) 10.1007/978-3-030-00934-2_36 Sci-Hub
N. Eckstein et al., "Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila melanogaster." Cell 187, 2574-2594 (2024) 10.1016/j.cell.2024.03.016 Sci-Hub

Upstream URL OK

https://zenodo.org/records/10676866
https://doi.org/10.1038/s41586-024-07686-5

Upstream license

CC BY 4.0, https://creativecommons.org/licenses/by/4.0/

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
min5	139,255	3,869,878	27.79	165.14	155.47	148.67	-0.03	0.05	16	0.95	Directed	Unipartite	root_id flow super_class cell_class cell_sub_class cell_type hemibrain_type hemilineage side nerve top_nt top_nt_conf	neuropil weight gaba ach glut oct ser da	149.3 MiB	222.7 MiB	220.8 MiB	228.2 MiB
all	139,255	16,847,997	120.99	373.73	519.84	185.17	-0.04	0.12	17	0.99	Directed	Unipartite	root_id flow super_class cell_class cell_sub_class cell_type hemibrain_type hemilineage side nerve top_nt top_nt_conf	neuropil weight gaba ach glut oct ser da	556.8 MiB	951.6 MiB	940.4 MiB	948.3 MiB
synapses_all	139,255	16,848,018	120.99	373.73	519.84	185.17	-0.04	0.12	17	0.99	Directed	Unipartite	root_id flow super_class cell_class cell_sub_class cell_type hemibrain_type hemilineage side nerve top_nt top_nt_conf	neuropil weight cleft_score connection_score gaba ach glut oct ser da	706.0 MiB	1.124 GiB	1.109 GiB	1.126 GiB

Ridiculograms^*

^* These are automatically generated force-directed visualizations, and can be quite meaningless for networks both big and small. They should not be taken seriously as sources of scientific insight. See here for a discussion.