platynereis_connectome — Platynereis dumerilii larval connectome (2025)

Description

Whole-body synaptic connectome of a three-day-old (72 hours post fertilization) larva of the marine annelid worm Platynereis dumerilii, which has a head, three trunk segments, and a pygidium. All cells were traced and annotated by Verasztó et al. in a serial-section transmission electron microscopy volume of 4,846 layers of 40 nm sections spanning the entire body of a larva, using the CATMAID software. The synapses are chemical (no gap junctions were identified) and monadic, i.e. each connects one presynaptic neuron to one postsynaptic cell.

Nodes are cells (neurons and the effector cells they innervate, such as muscles, ciliated cells, and glands) or neurite fragments that could not be attached to a cell with a soma, and a directed edge goes from a presynaptic to a postsynaptic cell, weighted by the number of synapses between them. The network is the connectome graph of Figure 2 of the paper, as provided in its source data. (An earlier version of the connectome, with 2,728 nodes, was distributed with the 2020 preprint of the paper.)

The network has the following properties:

Nodes: name, the name of the cell in CATMAID, which for most neurons indicates its cell type and side; skid, the skeleton identifier in the CATMAID database; celltype, the cell-type annotation in CATMAID (e.g. "celltype1"; "not_celltype" if the cell was not assigned to a cell type), which are described in Supplementary file 1 of the paper; class, the cell class ("sensory neuron", "interneuron", "motoneuron", "effector", "fragmentum" for fragments, or "other"); segment, the body region of the soma ("episphere" for the head, "segment_0" to "segment_3", "pygidium", or "fragment"); side, the body side of the soma ("left_side", "right_side", "middle", or "other"); module and module_name, the module of the cell, obtained by the authors with the Leiden community detection algorithm, numbered from 1 and named after their main effector organs or anatomical characters (e.g. "mech (l)", "NS", "ciliomotor"; empty for some modules).
Edges: weight, the number of synapses.

Tags

Biological Connectome Weighted Metadata

Citation

C. Verasztó, S. Jasek, M. Gühmann, L. A. Bezares-Calderón, E. A. Williams, R. Shahidi, G. Jékely, "Whole-body connectome of a segmented annelid larva." eLife 13, RP97964 (2025) 10.7554/eLife.97964 Sci-Hub
C. Verasztó, S. Jasek, M. Gühmann, R. Shahidi, N. Ueda, J. D. Beard, S. Mendes, K. Heinz, L. A. Bezares-Calderón, E. Williams, G. Jékely, "Whole-animal connectome and cell-type complement of the three-segmented Platynereis dumerilii larva." bioRxiv 2020.08.21.260984 (2020) 10.1101/2020.08.21.260984 Sci-Hub

Upstream URL OK

https://elifesciences.org/articles/97964

Upstream license

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

Networks

Tip: hover over a column header 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
platynereis_connectome	2,675	14,066	5.26	12.33	23.27	18.53	0.03	0.11	12	1.00	Directed	Unipartite	name skid celltype class segment side module module_name	weight	64 KiB	99 KiB	98 KiB	93 KiB