celegans_2019 — Complete C. elegans neurons (2019)

Description

Whole-animal connectomes of both sexes of the nematode Caenorhabditis elegans, the adult hermaphrodite and the adult male, reconstructed by S. J. Cook and collaborators from serial-section electron microscopy (EM) series, including both new reconstructions and a re-analysis of the original EM material of J. G. White and others. Nodes are cells: neurons, as well as the muscles and other end organs that they innervate. Edges are either chemical synapses (directed, from the pre-synaptic to the post-synaptic cell) or gap junctions (electrical synapses, undirected). To cover the entire nervous system, the connectomes were assembled from several animals, and connections were added by extrapolation in regions where no EM data were available.

There are twelve networks, named <sex>_<type>[_<version>], for each sex (hermaphrodite, male) and connection type (chemical, gap_junction):

• no suffix: the connectome adjacency matrices, where the edge property connectivity is the total number of EM serial sections in which the connection is observed, which accounts for both the number and the size of the synapses.
• _corrected: corrected versions of the connectome matrices, released by the authors in July 2020.
• _synapse: the synapse adjacency matrices, where the edge property synapses is the number of synapses scored between each pair of cells. These do not take into account the size of the synapses, include only connections scored on electron micrographs, and do not include connections inserted by extrapolation; hence some cells that are connected in the other networks are not connected here.

The networks have the following properties:

• (Node) name: the name of the cell.
• (Node) node_type: the cell category (e.g. sensory neurons, interneurons, motor neurons, pharynx, bodywall muscles, other end organs, sex-specific cells).
• (Node) node_subtype: a sub-category for some cells (e.g. head, sublateral or body motor neurons; empty otherwise). node_type and node_subtype are not available in male_chemical_synapse and male_gap_junction_synapse.
• (Edge) connectivity or synapses: as described above.

Tags

Biological Connectome Weighted

Added

2020-08-11

Citation

• Cook et al., "Whole-animal connectomes of both Caenorhabditis elegans sexes." Nature 571, 63-71 (2019) 10.1038/s41586-019-1352-7 Sci-Hub

Upstream URL OK

https://wormwiring.org/pages/adjacency.html

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

Show all columns

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
male_chemical	575	5,306	9.23	15.62	30.34	217.62	0.27	0.30	9	0.97	Directed	Unipartite	node_type node_subtype name	connectivity	20 KiB	33 KiB	34 KiB	29 KiB
male_gap_junction	585	1,755	6.00	6.72	16.41	124.49	0.23	0.22	17	0.83	Undirected	Unipartite	node_type node_subtype name	connectivity	15 KiB	21 KiB	21 KiB	18 KiB
hermaphrodite_chemical	453	4,879	10.77	16.41	29.45	148.18	0.12	0.26	7	0.98	Directed	Unipartite	node_type node_subtype name	connectivity	17 KiB	28 KiB	29 KiB	24 KiB
hermaphrodite_gap_junction	468	1,447	6.18	6.05	14.72	223.74	0.14	0.19	34	0.98	Undirected	Unipartite	node_type node_subtype name	connectivity	12 KiB	17 KiB	17 KiB	15 KiB
male_chemical_synapse	514	3,531	6.87	16.40	29.74	14.03	0.28	0.33	5	0.64	Directed	Unipartite	name	synapses	15 KiB	25 KiB	25 KiB	20 KiB
male_gap_junction_synapse	514	2,363	9.19	13.66	15.96	24.27	0.21	0.22	10	0.58	Undirected	Unipartite	name	synapses	14 KiB	20 KiB	20 KiB	17 KiB
hermaphrodite_chemical_synapse	468	3,701	7.91	16.75	27.88	5.39	0.10	0.27	5	0.67	Directed	Unipartite	node_type node_subtype name	synapses	15 KiB	24 KiB	25 KiB	21 KiB
hermaphrodite_gap_junction_synapse	466	2,056	8.82	11.72	13.87	13.33	0.10	0.18	9	0.60	Undirected	Unipartite	node_type node_subtype name	synapses	13 KiB	19 KiB	19 KiB	16 KiB
male_chemical_corrected	575	5,306	9.23	15.62	30.34	217.62	0.27	0.30	9	0.97	Directed	Unipartite	node_type node_subtype name	connectivity	21 KiB	34 KiB	34 KiB	29 KiB
male_gap_junction_corrected	586	1,758	6.00	6.71	16.46	107.44	0.24	0.22	17	0.83	Undirected	Unipartite	node_type node_subtype name	connectivity	15 KiB	22 KiB	21 KiB	18 KiB
hermaphrodite_chemical_corrected	454	4,879	10.75	16.43	29.45	148.18	0.12	0.26	7	0.98	Directed	Unipartite	node_type node_subtype name	connectivity	17 KiB	28 KiB	29 KiB	24 KiB
hermaphrodite_gap_junction_corrected	469	1,450	6.18	6.09	14.80	224.82	0.14	0.19	34	0.98	Undirected	Unipartite	node_type node_subtype name	connectivity	12 KiB	17 KiB	17 KiB	15 KiB

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.