fly_manc — Male fly adult nerve cord (2024)

Description

The connectome of the ventral nerve cord (VNC, the fly's analog of the spinal cord) of an adult male fruit fly Drosophila melanogaster, the "Male Adult Nerve Cord" (MANC) data set, reconstructed by the FlyEM project at the Janelia Research Campus and collaborators from focused ion beam scanning electron microscopy (FIB-SEM) images, with automated segmentation and synapse detection followed by extensive manual proofreading, and annotated systematically by the Cambridge Drosophila Connectomics Group. Nodes are neurons, and a directed edge $(i, j)$ indicates chemical synapses from neuron $i$ (presynaptic) to neuron $j$ (postsynaptic). This is release v1.0 (June 2023) of the data set, as exported by the authors from neuPrint: the 23,188 neurons with status "Traced" (the proofread neurons) and the connections between them.

There are three networks of v1.0:

traced_min5: only the pairs of neurons with at least five synapses are considered connected, since weak connections are unreliable, and for consistency with the flywire, fly_banc and fly_male_cns entries. These are 1,360,021 of the 5,243,574 connected pairs, carrying 24.0 million of their 30.7 million synapses.
traced_all: all connections, without threshold on the number of synapses.
traced_roi: all connections, split according to the primary region of interest (ROI, i.e. neuropil or nerve) where the synapses reside, so that the same pair of neurons may be connected by several parallel edges, one per ROI; synapses outside the primary ROIs have the ROI NotPrimary.

All networks of v1.0 have the same nodes, so that neurons without connections (with at least five synapses, in traced_min5) are isolated nodes. Self-loops are synapses of a neuron onto itself (autapses).

The entry also contains two networks of the later release v1.2 of the data set, which is not available as a connection table, but as a table of the individual synaptic connections ("synapse partners": 87 million pairs of a presynaptic T-bar and a postsynaptic density) with the confidence of the automated detection of each side (a value between 0 and 1). They are aggregated here into one weighted edge per pair of neurons:

v1.2_minconf0: all the synaptic connections of the table. Despite its name ("minconf-0.0"), the table only contains presynaptic T-bars with a confidence of at least 0.75 and postsynaptic densities with a confidence of at least 0.2; this corresponds to the "high recall" weights (weightHR) of neuPrint.
v1.2: only the synaptic connections whose postsynaptic density has a confidence of at least 0.4, the threshold that neuPrint uses for its default connection weights (postHighAccuracyThreshold in the metadata of the MANC database). The connection tables of v1.0 above have these default weights: for instance, the 136 synaptic connections of the table from neuron 10000 to neuron 14882 are 122 with this threshold, the weight of the pair in v1.0. (neuPrint also has "high precision" weights, weightHP, with confidences of at least 0.7 for both sides, which are not included.)

Their nodes are the 27,046 segments that have annotations in the neuroglancer segment properties of v1.2 published with the table (neurons, including sensory and motor neurons, and a few hundred glia; v1.2 has no export of the neuPrint neuron table with statuses as v1.0 has), and their edges are the synapses between them; the synaptic connections with the other segments (51 million of the 87 million) are left out. The v1.2 annotations are less detailed than those of v1.0, and are encoded as tags in neuroglancer (with underscores instead of spaces, e.g. descending_neuron). The later annotation releases v1.2.1 and v1.2.3 (in neuPrint) are not included.

The networks of v1.0 have the following properties:

(Node) body_id: the neuron's identifier in the data set (neuPrint body ID).
(Node) type, systematic_type: the cell type of the neuron (e.g. DNp01), and its systematic name (e.g. DNlt002); empty if not assigned.
(Node) instance: the neuron's instance name, typically the cell type followed by the side or segment (e.g. IN13B025_T2_L).
(Node) class, subclass: coarser classifications of the neuron (e.g. descending neuron, intrinsic neuron); empty if not assigned.
(Node) status_label: the proofreading status of the neuron (e.g. Roughly traced).
(Node) soma_side, root_side: the side of the neuron's soma, or for neurons without soma in the volume, of the place where they enter it (LHS, RHS, Midline, ...); empty if not assigned.
(Node) soma_neuromere: the neuromere (segment) of the neuron's soma (e.g. T1, A2); empty if not assigned.
(Node) hemilineage: the developmental hemilineage of the neuron; empty if not assigned.
(Node) birthtime: the developmental birth time of the neuron (primary, early secondary, secondary); empty if not assigned.
(Node) entry_nerve, exit_nerve: the nerve through which the neuron enters or exits the nerve cord; empty or None if none.
(Node) origin, target: the region where the neuron's inputs come from and where its outputs go (e.g. brain, LegNpT1_R); empty if not assigned.
(Node) long_tract: the longitudinal tract of the neuron; empty if not assigned.
(Node) serial_motif: the type of the neuron's serial (segmentally repeated) homology; empty if not assigned.
(Node) modality, receptor_type: the sensory modality and receptor type of sensory neurons; empty if not assigned.
(Node) transmission: annotations of electrical or neurosecretory transmission; empty if none.
(Node) group, serial: the identifiers of the neuron's group of left-right homologs and of its set of serial homologs (-1 if none).
(Node) predicted_nt, predicted_nt_prob: the neurotransmitter predicted from the neuron's synapses, and its probability (empty and NaN if not available).
(Node) pre, post: the numbers of presynaptic sites and of postsynaptic densities of the neuron.
(Edge) weight (edges): the number of synapses from $i$ to $j$ (in the given ROI, in traced_roi).
(Edge) roi (edges, traced_roi only): the primary ROI where the synapses are located.

The networks of v1.2 have the following properties:

(Node) body_id: the neuron's identifier (segment ID of v1.2).
(Node) type: the cell type of the neuron; empty if not assigned.
(Node) class, subclass, hemilineage, birthtime, soma_side, soma_neuromere, entry_nerve, exit_nerve, origin, target, long_tract, serial_motif, modality: as above, from the tags of the segment properties; empty if not assigned.
(Node) pre, post: the numbers of presynaptic sites and of postsynaptic densities of the neuron, as given by the segment properties (all those of the synapse table, including the ones with any partner, without the threshold of v1.2).
(Edge) weight (edges): the number of synaptic connections from $i$ to $j$ (of the given confidence).
(Edge) mean_conf_pre, mean_conf_post (edges): the mean detection confidence of their presynaptic T-bars and of their postsynaptic densities.

Tags

Biological Connectome Weighted Multigraph Metadata

Added

2026-10-27

Citation

S. Takemura et al., "A connectome of the male Drosophila ventral nerve cord." eLife 13, RP97769 (2024) 10.7554/eLife.97769 Sci-Hub
E. C. Marin et al., "Systematic annotation of a complete adult male Drosophila nerve cord connectome reveals principles of functional organisation." eLife 13, RP97766 (2024) 10.7554/eLife.97766 Sci-Hub

Upstream URL OK

https://www.janelia.org/manc-connectome
https://console.cloud.google.com/storage/browser/manc-seg-v1p2

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
traced_min5	23,188	1,360,021	58.65	119.86	223.46	10.26	-0.04	0.12	6	1.00	Directed	Unipartite	body_id type systematic_type instance class subclass status_label soma_side root_side soma_neuromere hemilineage birthtime entry_nerve exit_nerve origin target long_tract serial_motif modality receptor_type transmission predicted_nt group serial predicted_nt_prob pre post	weight	3.5 MiB	7.0 MiB	7.1 MiB	6.5 MiB
traced_all	23,188	5,243,574	226.13	417.30	712.65	8.14	0.01	0.21	6	1.00	Directed	Unipartite	body_id type systematic_type instance class subclass status_label soma_side root_side soma_neuromere hemilineage birthtime entry_nerve exit_nerve origin target long_tract serial_motif modality receptor_type transmission predicted_nt group serial predicted_nt_prob pre post	weight	8.7 MiB	20.4 MiB	20.4 MiB	18.8 MiB
traced_roi	23,188	6,173,185	266.22	547.72	712.65	8.36	0.06	0.23	6	1.00	Directed	Unipartite	body_id type systematic_type instance class subclass status_label soma_side root_side soma_neuromere hemilineage birthtime entry_nerve exit_nerve origin target long_tract serial_motif modality receptor_type transmission predicted_nt group serial predicted_nt_prob pre post	weight roi	12.1 MiB	32.9 MiB	30.2 MiB	25.9 MiB
v1.2_minconf0	27,046	6,168,749	228.08	478.63	793.99	22.10	0.01	0.22	10	1.00	Directed	Unipartite	body_id type class subclass hemilineage birthtime soma_side soma_neuromere entry_nerve exit_nerve origin target long_tract serial_motif modality pre post	weight mean_conf_pre mean_conf_post	47.2 MiB	95.1 MiB	93.8 MiB	107.0 MiB
v1.2	27,046	5,407,280	199.93	419.44	714.41	12.41	0.00	0.20	9	0.99	Directed	Unipartite	body_id type class subclass hemilineage birthtime soma_side soma_neuromere entry_nerve exit_nerve origin target long_tract serial_motif modality pre post	weight mean_conf_pre mean_conf_post	40.8 MiB	82.6 MiB	81.5 MiB	92.7 MiB