celegans_contactome — C. elegans nerve ring membrane contacts (2021)

Description

Membrane contact networks ("contactomes") of the nerve ring, the main neuropil of the brain of the nematode Caenorhabditis elegans, reconstructed by Brittin et al. from the serial-section electron microscopy (EM) images of two animals, an L4 larva (series JSH) and an adult hermaphrodite (series N2U), originally imaged by White et al. (1986). The neurites of the cells were segmented in each EM section, and the membrane contacts between them were measured. Nodes are cells (neurons, identified by their standard names, e.g. AVAL), and an edge indicates that the membranes of two cells are adjacent.

There are two kinds of networks:

• l4, adult: the membrane contacts of each animal, aggregated over the EM sections (410 sections for the L4 animal, 302 for the adult). These are undirected.
• reference_*: the authors' graphs of the connections classified by their reproducibility across the four available nerve ring sides (left and right of the two animals, with left and right cells mapped onto each other): *_delta1 to *_delta4 contain the connections found in exactly $\delta$ = 1 to 4 of the four sides:
• reference_contact_delta*: membrane contacts, after removing the contacts below the 35th percentile of contact area (reference_contact_delta4_classes: the same for $\delta=4$, with the left and right cells of each class merged into a single node);
• reference_chemical_delta*: chemical synapses (directed), computed by the authors on the membrane contacts with $\delta=4$; reference_chemical_delta*_pruned leaves out the C1 polyadic synapses (see the paper);
• reference_gap_delta*: gap junctions (undirected), likewise.

The reference graphs include the nodes PVR, PVNL, HSNL, PVR., HSNR, SABD, VB02, PLNL, PLNR and PVNR, which the authors remove for their "restricted" data set (they are kept here, as in the upstream files). The membrane contacts of individual animals with their synapses are also available upstream as SQL databases, which are not included here (the synapses of both animals are in the celegans_2019 entry).

The networks have the following properties:

• name: the name of the cell (or of the cell class, in reference_contact_delta4_classes).
• weight (edges): in l4 and adult, the total membrane contact area in μm² (the number of adjacent pixels, scaled by $4.5\times 10^{-4}$); in the reference graphs, the average over the $\delta$ sides where the connection is found of the membrane contact in pixels (contacts) or of the number of EM sections with synapses (chemical synapses and gap junctions), as given by the authors (whose documentation describes it as the total).
• pixels (edges, l4 and adult only): the total membrane contact in pixels.
• sections (edges, l4 and adult only): the number of EM sections in which the two cells are in contact.

Tags

Biological Connectome Weighted Metadata

Citation

• C. A. Brittin, S. J. Cook, D. H. Hall, S. W. Emmons, N. Cohen, "A multi-scale brain map derived from whole-brain volumetric reconstructions." Nature 591, 105-110 (2021) 10.1038/s41586-021-03284-x Sci-Hub

Upstream URL OK

https://doi.org/10.5281/zenodo.4763083

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

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
l4	181	4,763	52.63	18.67	58.93	1.55	0.08	0.45	3	1.00	Undirected	Unipartite	name	weight pixels sections	42 KiB	64 KiB	61 KiB	49 KiB
adult	185	5,245	56.70	19.12	62.63	1.47	0.05	0.46	3	1.00	Undirected	Unipartite	name	weight pixels sections	46 KiB	69 KiB	67 KiB	53 KiB
reference_contact_delta1	179	917	10.25	6.53	12.60	1.81	-0.25	0.08	5	1.00	Undirected	Unipartite	name	weight	7 KiB	11 KiB	11 KiB	9 KiB
reference_contact_delta2	175	617	7.05	5.13	9.31	3.03	-0.18	0.07	6	1.00	Undirected	Unipartite	name	weight	7 KiB	10 KiB	9 KiB	8 KiB
reference_contact_delta3	161	411	5.11	3.66	6.25	5.28	-0.24	0.07	7	1.00	Undirected	Unipartite	name	weight	6 KiB	9 KiB	8 KiB	7 KiB
reference_contact_delta4	167	1,258	15.07	10.85	21.55	4.16	-0.15	0.27	6	1.00	Undirected	Unipartite	name	weight	9 KiB	14 KiB	14 KiB	11 KiB
reference_contact_delta4_classes	93	806	17.33	7.73	20.40	3.75	0.13	0.39	4	1.00	Undirected	Unipartite	name	weight	6 KiB	9 KiB	9 KiB	8 KiB
reference_chemical_delta1	180	1,403	7.79	10.09	17.87	2.36	-0.19	0.15	5	1.00	Directed	Unipartite	name	weight	7 KiB	12 KiB	11 KiB	9 KiB
reference_chemical_delta1_pruned	165	292	1.77	3.45	5.20	11.18	-0.05	0.09	8	0.81	Directed	Unipartite	name	weight	5 KiB	7 KiB	7 KiB	5 KiB
reference_chemical_delta2	160	510	3.19	4.58	7.72	7.06	-0.09	0.10	7	1.00	Directed	Unipartite	name	weight	5 KiB	8 KiB	8 KiB	6 KiB
reference_chemical_delta2_pruned	152	287	1.89	3.16	4.42	12.61	-0.15	0.07	9	0.92	Directed	Unipartite	name	weight	5 KiB	7 KiB	7 KiB	5 KiB
reference_chemical_delta3	148	277	1.87	2.58	4.05	21.38	-0.08	0.09	12	1.00	Directed	Unipartite	name	weight	5 KiB	7 KiB	7 KiB	5 KiB
reference_chemical_delta3_pruned	141	202	1.43	2.32	3.25	23.83	-0.02	0.08	11	0.87	Directed	Unipartite	name	weight	5 KiB	6 KiB	6 KiB	5 KiB
reference_chemical_delta4	151	468	3.10	5.21	7.90	9.09	-0.03	0.16	8	1.00	Directed	Unipartite	name	weight	5 KiB	8 KiB	7 KiB	6 KiB
reference_chemical_delta4_pruned	149	443	2.97	5.05	7.54	9.82	-0.02	0.16	8	1.00	Directed	Unipartite	name	weight	5 KiB	8 KiB	7 KiB	6 KiB
reference_gap_delta1	157	329	4.19	2.96	5.05	6.60	-0.09	0.05	8	0.99	Undirected	Unipartite	name	weight	5 KiB	7 KiB	6 KiB	5 KiB
reference_gap_delta2	107	109	2.04	1.30	1.81	87.85	-0.01	0.07	16	0.79	Undirected	Unipartite	name	weight	4 KiB	5 KiB	4 KiB	4 KiB
reference_gap_delta3	74	60	1.62	0.98	1.00	53.91	-0.03	0.00	11	0.46	Undirected	Bipartite	name	weight	3 KiB	4 KiB	4 KiB	3 KiB
reference_gap_delta4	101	103	2.04	1.50	2.68	92.92	0.08	0.07	17	0.80	Undirected	Unipartite	name	weight	4 KiB	5 KiB	4 KiB	4 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.