mouse_retina — Mouse retina inner plexiform layer contacts (2013)

Description

Undirected network of physical contacts between neurons of the inner plexiform layer of the mouse retina, from the connectomic reconstruction of Helmstaedter et al. A block of retina (about 114 x 80 x 132 micrometres) was imaged by serial block-face electron microscopy; the neurons were reconstructed by combining skeleton tracing by about 200 (crowd-sourced) student annotators with machine-learning volume segmentation, and the contacts between the reconstructed cells were then detected automatically. Nodes are cells (950 classified neurons, plus 173 cells without annotations), and each edge is one contact between two cells, located in space and weighted by its area, so that most pairs of cells are joined by many parallel edges (577,350 contacts between 90,811 pairs of cells). Contacts are not necessarily synapses.

The network has the following properties:

Nodes: name, the cell identifier; coarse, the coarse cell class ("gc" ganglion cell, "bc" bipolar cell, "nac" narrow-field amacrine cell, "mwac" medium/wide-field amacrine cell, "other", or "NA"); designation, the cell type assigned in the publication (e.g. "bc48-88", "gc10-40"); volgyi_type and macneil_type, the corresponding ganglion cell type in the classification of Völgyi et al. and amacrine cell type in the classification of MacNeil et al.; certainty, the certainty of the classification ("H" high, "M" medium, "L" low); x, y, z, the position of the cell body, in micrometres (0 for the unannotated cells).
Edges: x, y, z, the position of the contact, in micrometres; area, the contact area, in square micrometres.

The data were obtained by OpenConnectome from the processed version of the supplementary data in E. Jonas' circuitdata repository. The data were obtained from the graph collection of the Open Connectome Project (now NeuroData), whose servers are offline, via the Internet Archive.

Tags

Biological Connectome Weighted Multigraph Spatial Metadata

Citation

M. Helmstaedter, K. L. Briggman, S. C. Turaga, V. Jain, H. S. Seung, W. Denk, "Connectomic reconstruction of the inner plexiform layer in the mouse retina." Nature 500, 168-174 (2013) 10.1038/nature12346 Sci-Hub

Upstream URL OK

https://web.archive.org/web/20160420202242/http://openconnecto.me/graph-services/download/

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
mouse_retina	1,123	577,350	1028.23	1104.40	254.97	3.18	0.02	0.61	4	0.96	Undirected	Unipartite	certainty coarse designation macneil_type name volgyi_type x y z	area x y z	7.7 MiB	11.5 MiB	11.2 MiB	9.0 MiB