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fly_optic_lobe — Male fly optic lobe (2025)

Description

The connectome of the right optic lobe (the visual system) of an adult male fruit fly Drosophila melanogaster, together with the parts of the central brain that it connects to, 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. The authors identified over 700 cell types among the roughly 53,000 neurons of the optic lobe. Nodes are neurons (segments of the reconstruction), and a directed edge $(i, j)$ indicates chemical synapses from neuron $i$ (presynaptic) to neuron $j$ (postsynaptic). The data come from the two releases of the data set that the authors exported as flat files, v1.1 (September 2024, with further proofreading and refined annotations) and v1.0.1 (August 2024).

Only synapses detected with a confidence of at least 0.5 are included, as in the authors' published data. There are six networks, named <release>_<nodes>_<threshold>:

  • *_primary_min5, *_primary_all: the networks between the proofread bodies, from the authors' "primary-only" connection table. Its nodes are the bodies (53,735 in v1.1, 53,420 in v1.0.1) with the proofreading status "Roughly traced", "Prelim Roughly traced", "Leaves", "PRT Orphan" (together the "Traced" neurons of neuPrint) or "Primary Anchor" (large segments that were not fully traced); the upstream documentation does not describe this table, this is what it contains. In *_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; in *_all all connections are included. In v1_1_primary_min5, these are 1,555,385 of the 6,497,418 connected pairs, carrying 17.6 million of their 26.6 million synapses.
  • *_segments_all: all 10.3 million segments of the reconstruction, most of them small fragments that could not be attached to a neuron, with all their connections (22.3 million connected pairs and 49.5 million synapses). The table also contains a few connections with the unsegmented background (body 0; 198 pairs with 207 synapses), which are left out. To keep these networks manageable, their nodes only have the properties body_id, status_label, type, instance, class, pre and post.

All networks of a release and node set have the same nodes, so that neurons without connections (with at least five synapses, in *_min5) are isolated nodes. Self-loops are synapses of a neuron onto itself (autapses). The annotations and neurotransmitter predictions are those of the corresponding release, from its neuPrint tables.

The networks have the following properties:

  • body_id: the neuron's identifier in the data set (neuPrint body ID).
  • status_label: the proofreading status of the body (e.g. Roughly traced, Primary Anchor; empty for unproofread fragments).
  • type: the cell type of the neuron (e.g. Mi1, T4a); empty if not assigned.
  • instance: the neuron's instance name, typically the cell type followed by the side (e.g. Mi1_R).
  • class: the coarse class of the neuron (e.g. optic, visual_projection, visual_centrifugal, sensory); empty if not assigned.
  • flywire_type: the matched cell type in the female brain connectome FlyWire (see the flywire entry); empty if not assigned (always empty in v1.0.1, which has no such annotations).
  • hemilineage: the developmental hemilineage of the neuron; empty if not assigned (always empty in v1.0.1).
  • neurotransmitter: the consensus neurotransmitter of the neuron's cell type, from the predictions and the literature (unclear if ambiguous); empty if not available.
  • predicted_nt, predicted_nt_confidence: the neurotransmitter predicted from the neuron's own synapses, and the confidence of that prediction (empty and NaN if not available).
  • hex1, hex2: the coordinates of the column of the medulla's hexagonal grid (i.e. the point of the visual field) assigned to the neuron, for the columnar cell types (-1 if not assigned).
  • soma_x, soma_y, soma_z: the position of the neuron's soma in the volume, in voxels of 8 nm (NaN if not known).
  • pre, post: the numbers of presynaptic sites and of postsynaptic densities of the neuron.
  • weight (edges): the number of synapses from $i$ to $j$.
Tags
Biological Connectome Weighted Metadata
Citation
Upstream URL OK
https://www.janelia.org/project-team/flyem/optic-lobe
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
v1_1_primary_min5 53,735 1,555,385 28.95 116.43 163.67 10.69 -0.04 0.03 8 0.97 Directed Unipartite body_id status_label type instance class flywire_type hemilineage neurotransmitter predicted_nt predicted_nt_confidence hex1 hex2 soma_x soma_y soma_z pre post weight 4.5 MiB 8.5 MiB 8.3 MiB 7.9 MiB
v1_1_primary_all 53,735 6,497,418 120.92 351.70 520.96 156.14 -0.05 0.09 14 0.98 Directed Unipartite body_id status_label type instance class flywire_type hemilineage neurotransmitter predicted_nt predicted_nt_confidence hex1 hex2 soma_x soma_y soma_z pre post weight 13.5 MiB 29.2 MiB 26.8 MiB 25.2 MiB
v1_1_segments_all 10,314,236 22,249,949 2.16 74.17 523.76 21390.94 -0.05 0.02 35 0.99 Directed Unipartite body_id status_label type instance class pre post weight 96.9 MiB 152.5 MiB 145.8 MiB 159.4 MiB
v1_0_1_primary_min5 53,420 1,553,478 29.08 116.60 163.56 10.68 -0.04 0.03 8 0.97 Directed Unipartite body_id status_label type instance class flywire_type hemilineage neurotransmitter predicted_nt predicted_nt_confidence hex1 hex2 soma_x soma_y soma_z pre post weight 4.5 MiB 8.4 MiB 8.3 MiB 7.9 MiB
v1_0_1_primary_all 53,420 6,492,366 121.53 352.08 520.74 156.14 -0.05 0.09 14 0.98 Directed Unipartite body_id status_label type instance class flywire_type hemilineage neurotransmitter predicted_nt predicted_nt_confidence hex1 hex2 soma_x soma_y soma_z pre post weight 13.5 MiB 29.2 MiB 26.8 MiB 25.1 MiB
v1_0_1_segments_all 10,318,164 22,258,367 2.16 74.12 523.58 21389.35 -0.05 0.02 35 0.99 Directed Unipartite body_id status_label type instance class pre post weight 96.6 MiB 152.2 MiB 145.6 MiB 159.4 MiB