logo Netzschleuder network catalogue, repository, and centrifuge

mouse_mesoscale — Mouse brain mesoscale connectome (2014)

Description

Networks of axonal projections between regions of the mouse brain, from the Allen Mouse Brain Connectivity Atlas of Oh et al. (Allen Institute for Brain Science). In each of 469 experiments, an adeno-associated viral tracer expressing EGFP was injected into one location of the right hemisphere of a C57BL/6J mouse, and the fluorescently labelled axons were imaged brain-wide by serial two-photon tomography, registered to the Allen Reference Atlas, and segmented. The brain was divided into 295 non-overlapping regions (plus fiber tracts) in each hemisphere.

  • projections: bipartite network between the 469 injection experiments and the 592 target regions (296 per hemisphere, including "fiber tracts"), from Supplementary Table 2. An edge connects an experiment to each target region where projections were detected, weighted by the normalized projection volume (the number of segmented signal pixels in the target region divided by that in the injection volume). Target regions are distinguished by hemisphere, ipsilateral (right) or contralateral (left) to the injection. 106 entries of the source table have the value -1, which is not documented, and are omitted.
  • model: directed network of the 213 regions on each hemisphere (426 nodes) from Supplementary Tables 3 and 4, obtained by the authors by fitting a linear model of connectivity, in which the projection signal of each experiment is a combination of the projections of the source regions covered by its injection. Edges point from a source region (on the right hemisphere) to an ipsilateral or contralateral target region, for every non-zero fitted connection strength (32,822 edges, 16,954 of them ipsilateral). Nodes on the left (contralateral) hemisphere therefore have no outgoing edges.

The networks have the following properties:

  • Region nodes: name, the region acronym (for experiment nodes, the image series identifier) in the Allen Reference Atlas; full_name, the region name; major_region, the major brain division (e.g. "Isocortex", "Thalamus"; acronyms such as "ISOCORTEX" or "TH" in projections); hemisphere, "ipsilateral" (right) or "contralateral" (left); voxel_count, the volume of the region in voxels of the reference atlas (100 micrometres on each side).
  • Experiment nodes (projections): is_injection, whether the node is an injection experiment (otherwise it is a region); image_series_id and specimen, the identifiers of the experiment and the animal; primary_structure and secondary_structure, the regions containing the injection site; injection_volume, in cubic millimetres; major_region, the major division of the injection site.
  • Edges: weight, the normalized projection volume (projections) or the fitted normalized connection strength (model); pvalue, the p-value of the fitted connection strength (NaN when it could not be computed) (model only); distance, the distance between the centres of mass of the two regions, in micrometres (model only).
Tags
Biological Connectome Weighted Metadata
Citation
Upstream URL OK
https://doi.org/10.1038/nature13186
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
projections 1,061 238,510 449.59 88.64 462.07 0.59 -0.49 0.00 3 1.00 Undirected Bipartite is_injection name hemisphere major_region image_series_id specimen primary_structure secondary_structure injection_volume full_name voxel_count weight 1.6 MiB 2.0 MiB 2.1 MiB 1.6 MiB
model 426 32,822 77.05 98.10 169.60 0.83 -0.31 0.49 2 1.00 Directed Unipartite name hemisphere major_region full_name voxel_count weight pvalue distance 689 KiB 949 KiB 944 KiB 999 KiB