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microns_mm3 — MICrONS mouse visual cortex (2023-2025)

Description

The synaptic connectome of the neurons in a cubic millimeter of mouse visual cortex, from the IARPA MICrONS project: a volume spanning all cortical layers of the primary visual cortex (VISp) and the higher visual areas VISrl, VISal and VISlm of an adult mouse, imaged with serial-section transmission electron microscopy, automatically segmented, with synapses detected automatically, and partially proofread. Nodes are neurons, and a directed edge $(i, j)$ indicates chemical synapses from neuron $i$ (presynaptic) to neuron $j$ (postsynaptic).

The networks are the three versions of the compilation of M. W. Reimann, which contains the synapses between the neurons with a cell body inside the larger of the two imaged subvolumes ("portion 65"), but no synapses from neurons outside it, named after the materialization (version) of the public MICrONS data, "minnie65_public", that they are based on:

  • v1412: version 3.0.0 of the compilation (August 2025), based on materialization v1412, with 50,948 neurons. It leaves out about 20,000 neurons near the periphery of the volume, whose connectivity is strongly affected by the boundary.
  • v1181: version 2.0.0 (September 2024), based on materialization v1181, with more proofread neurons and a newer cell type classification than v117 (71,981 neurons).
  • v117: version 1.0.0 (September 2023), based on materialization v117 (60,048 neurons), with the coarse cell classes of the Allen Institute.

Each version has also a network with one edge per synapse (the "full" representation of the compilation), named v1412_full, v1181_full and v117_full, with the same nodes: two neurons are connected by as many parallel edges as there are synapses between them (11.6, 13.5 and 10.1 million edges).

The version 3.0.0 has also a "distance-dependent control" (v1412_control): a random network generated by the author of the compilation as a null model, in which, for each pathway (combination of the layers and synapse classes of the presynaptic and postsynaptic neurons), the connection probability is an exponentially decaying function of the distance between the neurons fitted to the data. It contains only the 45,598 excitatory neurons of v1412 (the inhibitory neurons are left out of the control), and is unweighted (one edge per connected pair).

All versions leave out a few hundred cell bodies associated with several cell types (merges of several neurons). All connections are included, without threshold on the number of synapses (most connections in the cortex consist of one or two synapses). Note that only a small fraction of the neurons were proofread (see the properties status_axon and status_dendrite); the axons of the others are mostly incomplete, and their connections may contain errors of the automated segmentation.

The networks have the following properties:

  • (Node) root_id: the neuron's identifier (root ID) in the MICrONS data of that version.
  • (Node) cell_type: the type of the neuron, predicted from features of its soma and nucleus: in v1412 and v1181, the morphological type (m-type; e.g. L2a, L4b, L5ET, L6tall-a for excitatory neurons; PTC, DTC, STC and ITC for perisomatic-targeting, distal-targeting, sparsely-targeting and inhibitory-targeting inhibitory neurons); in v117, the coarse cell class (e.g. 23P, 4P, 5P_IT, 6CT, BC, MC).
  • (Node) classification_system (v1412 and v1181): excitatory_neuron or inhibitory_neuron.
  • (Node) synapse_class (v1412): whether the neuron is excitatory (EXC) or inhibitory (INH).
  • (Node) layer (v1412): the cortical layer of the neuron (2 to 6), derived from its type; empty for inhibitory neurons.
  • (Node) tentative_region (v117): the visual area of the neuron (visp, visrl, visal or vislm), which the author of the compilation warns is only a rough estimate.
  • (Node) status_axon, status_dendrite: whether the neuron's axon and dendrite were proofread (t) or not (f), for the neurons in the proofreading table of MICrONS; in v117, the proofreading status of the public release of the time: non (not proofread), clean (false merges removed) or extended (also false splits corrected); empty for the neurons that are not in that table, which were not proofread.
  • (Node) volume (v1412 and v1181): the volume of the neuron's nucleus, in µm³.
  • (Node) x, y, z: the position of the neuron's soma, in µm ($y$ increases with the cortical depth).
  • (Edge) weight: the number of synapses from $i$ to $j$ (not in the _full networks and in v1412_control).
  • (Edge) total_size, mean_size (v1181 and v117): the sum and the mean of the sizes of these synapses, as given by the synapse table of MICrONS (in voxels).
  • (Edge) synapse_id, size (_full networks): the identifier of the synapse in the synapse table of MICrONS, and its size (in voxels).
  • (Edge) syn_x, syn_y, syn_z, soma_distance (v1181_full and v117_full): the position of the synapse, in µm, and its distance from the soma of the postsynaptic neuron, in µm.

In v1412_control, the nodes have the properties root_id, cell_type (the m-type), synapse_class (EXC), layer, volume and x, y, z, as above.

The compilation's "valid" flag of the neurons, the identifiers of their cell bodies (supervoxel and nucleus IDs), and, in v117, their degrees (which the networks give), are left out. In the _full networks, the offsets of the synapses from the soma of the postsynaptic neuron (which follow from their positions) are left out. In v1412_control, a second set of coordinates of the neurons (X, Y, Z, not documented) and a few columns that are empty for almost all neurons (morphologies, spines, in-degrees) are left out.

Tags
Biological Connectome Weighted Multigraph Metadata
Added
2026-10-27
Citation
Upstream URL OK
https://zenodo.org/records/16744240
https://zenodo.org/records/13849415
https://zenodo.org/records/8364070
https://www.microns-explorer.org/cortical-mm3
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
Name Nodes Edges $\left<k\right>$ $\sigma_k$ $\lambda_h$ $\tau$ $r$ $c$ $\oslash$ $S$ Kind Mode NPs EPs gt GraphML GML csv
v1412 50,948 7,463,640 146.50 425.23 738.49 9.78 -0.17 0.09 5 1.00 Directed Unipartite root_id cell_type classification_system synapse_class layer status_axon status_dendrite volume x y z weight 11.6 MiB 27.3 MiB 25.0 MiB 22.4 MiB
v1181 71,981 9,005,438 125.11 375.49 710.52 18.42 -0.14 0.09 9 1.00 Directed Unipartite root_id cell_type classification_system status_axon status_dendrite volume x y z weight total_size mean_size 47.8 MiB 70.9 MiB 70.3 MiB 72.0 MiB
v117 60,048 6,965,260 115.99 312.34 614.76 23.55 -0.10 0.09 11 0.99 Directed Unipartite root_id cell_type tentative_region status_axon status_dendrite x y z weight total_size mean_size 38.4 MiB 57.7 MiB 57.2 MiB 58.2 MiB
v1412_full 50,948 11,554,859 226.80 846.15 738.49 11.59 -0.20 0.12 5 1.00 Directed Unipartite root_id cell_type classification_system synapse_class layer status_axon status_dendrite volume x y z synapse_id size 70.7 MiB 112.1 MiB 111.0 MiB 104.1 MiB
v1181_full 71,981 13,500,999 187.56 720.71 710.52 20.78 -0.17 0.11 9 1.00 Directed Unipartite root_id cell_type classification_system status_axon status_dendrite volume x y z synapse_id size syn_x syn_y syn_z soma_distance 279.1 MiB 421.2 MiB 406.0 MiB 380.3 MiB
v117_full 60,048 10,125,944 168.63 586.11 614.76 22.40 -0.13 0.12 11 0.99 Directed Unipartite root_id cell_type tentative_region status_axon status_dendrite x y z synapse_id size syn_x syn_y syn_z soma_distance 214.1 MiB 323.7 MiB 313.7 MiB 289.2 MiB
v1412_control 45,598 3,037,433 66.61 50.87 158.57 3.59 0.25 0.01 4 1.00 Directed Unipartite root_id cell_type synapse_class layer volume x y z 6.2 MiB 10.7 MiB 10.5 MiB 10.9 MiB