NeuroData's Graph DataBase

Lowering the barrier to entry for scalable neuroscience

Biologically derived graphs

Thanks to all who provided the raw data from which we derived these graphs. Every graph is annotated with a source attribute that denotes its origin.
Graphs are provided by default in graphML format. This is the only format that supports iterable attributes.
Consider using the graph conversion api for post-download conversion. Examples of how to load graphs using igraph can be found here.
Downloaded zip files must be unzipped using Linux unzip.

All data here can also be acquired directly from http://openconnecto.me/mrdata/static/graphs/.

Cat

Download url region # Nodes # Edges Graph Attrs Node Attrs Edge Attrs sensor project Source host url
Mixed.species_brain_1 brain 65 1139 source, region, DOI, sensor id Tract tracing studies www.jneurosci.org
  • 1 graph download model

Fly

Download url region # Nodes # Edges Graph Attrs Node Attrs Edge Attrs sensor project Source host url
Drosophila_medulla_1 medulla 1781 33641 info, source, region, DOI, sensor name, id post.z, post.x, post.y, pre.x, pre.y, pre.z, proofreading.details Electron Microscopy www.nature.com
  • 1 graph download model

Human

For a data description of the brain graph attributes click here.

Download url region # Nodes # Edges Graph Attrs Node Attrs Edge Attrs sensor project Source host url
Swu4_0025752_1_dti_ds00096 95 610 date, website, version, name id weight
Swu4_0025752_2_dti_ds00096 95 620 date, website, version, name id weight
Swu4_0025753_1_dti_ds00096 95 612 date, website, version, name id weight
Swu4_0025753_2_dti_ds00096 95 597 date, website, version, name id weight
Swu4_0025756_1_dti_ds00096 95 554 date, website, version, name id weight
Swu4_0025756_2_dti_ds00096 95 570 date, website, version, name id weight
Swu4_0025757_1_dti_ds00096 95 610 date, website, version, name id weight
Swu4_0025757_2_dti_ds00096 95 660 date, website, version, name id weight
Swu4_0025758_1_dti_ds00096 95 567 date, website, version, name id weight
Swu4_0025758_2_dti_ds00096 95 564 date, website, version, name id weight
Swu4_0025759_1_dti_ds00096 95 617 date, website, version, name id weight
Swu4_0025759_2_dti_ds00096 95 694 date, website, version, name id weight
Swu4_0025760_1_dti_ds00096 95 633 date, website, version, name id weight
Swu4_0025760_2_dti_ds00096 95 642 date, website, version, name id weight
Swu4_0025761_1_dti_ds00096 95 658 date, website, version, name id weight
Swu4_0025761_2_dti_ds00096 95 661 date, website, version, name id weight
Swu4_0025762_1_dti_ds00096 95 487 date, website, version, name id weight
Swu4_0025762_2_dti_ds00096 95 523 date, website, version, name id weight
Swu4_0025763_1_dti_ds00096 95 573 date, website, version, name id weight
Swu4_0025763_2_dti_ds00096 95 581 date, website, version, name id weight
Swu4_0025764_1_dti_ds00096 95 515 date, website, version, name id weight
Swu4_0025764_2_dti_ds00096 95 594 date, website, version, name id weight
Swu4_0025765_1_dti_ds00096 95 615 date, website, version, name id weight
Swu4_0025765_2_dti_ds00096 95 571 date, website, version, name id weight
Swu4_0025766_1_dti_ds00096 95 676 date, website, version, name id weight
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  • 25 of 66853 graph download models

Downsample factor:

Macaque

Download url region # Nodes # Edges Graph Attrs Node Attrs Edge Attrs sensor project Source host url
Rhesus_brain_1 cerebral cortex 242 4090 source, region, DOI, sensor name, id Tract tracing studies www.plosone.org
Rhesus_brain_2 brain 91 628 source, region, DOI, sensor name, id SLN_perc, Dist_mm Retrograde tracer www.core-nets.org
Rhesus_cerebral.cortex_1 cerebral cortex 91 1989 source, region, DOI, sensor name, id CASE, STATUS, BIBLIOGRAPHY, MONKEY, NEURONS, FLNe Retrograde tracer www.core-nets.org
Rhesus_interareal.cortical.network_2 interareal cortical network 93 2667 source, region, DOI, sensor name, id weight Retrograde tracer www.core-nets.org
  • 4 graph download models

Mouse

Download url region # Nodes # Edges Graph Attrs Node Attrs Edge Attrs sensor project Source host url
Mouse_brain_1 brain 213 21807 source, region, DOI, sensor name, id w_contra_weight, pvalue_contra_weight, w_ipsi_weight, pvalue_ipsi_weight Enhanced green fluorescent protein www.nature.com
Mouse_retina_1 retina 1123 577350 source, region, sensor name, designation, macneil_type, certainty, volgyi_type, coarse, y, x, z, id y, x, z, area Electron Microscopy github.com
Kasthuri_graph_v4 1029 1700 id, vid direction, synapse_id
Mouse_visual.cortex_1 cerebral cortex 29 44 info, source, region, DOI, sensor type1, id, type2 weight Electron microscopy www.nature.com
Mouse_visual.cortex_2 cerebral cortex 195 214 info, DOI, region, source, key, sensor type1, id, type2 weight Electron microscopy www.nature.com
  • 5 graph download models

Rat

Download url region # Nodes # Edges Graph Attrs Node Attrs Edge Attrs sensor project Source host url
Rattus.norvegicus_brain_1 brain 503 27667 source, region, sensor name, id weight Neuroanatomical experiments brancusi1.usc.edu
Rattus.norvegicus_brain_2 brain 503 30088 source, region, sensor name, id weight Neuroanatomical experiments brancusi1.usc.edu
Rattus.norvegicus_brain_3 brain 496 33020 source, region, sensor name, id weight Neuroanatomical experiments brancusi1.usc.edu
  • 3 graph download models

Worm

Download url region # Nodes # Edges Graph Attrs Node Attrs Edge Attrs sensor project Source host url
C.elegans_neural.male_1 neural 272 4451 source, region, DOI, sensor name, id electrical_weight, chemical_weight Electron Microscopy www.sciencemag.org
C.elegans.herm_pharynx_1 pharynx 279 3225 info, source, region, sensor name, cell_name, role, cell_class, neurotransmitters, id, soma_pos synapse_type, weight Electron Microscopy github.com
P.pacificus_neural.synaptic_1 neural synaptic 54 511 info, source, region, DOI, sensor name, id synapse.ID Electron Microscopy www.sciencedirect.com
P.pacificus_neural.synaptic_2 neural synaptic 50 611 info, source, region, DOI, sensor name, id synapse.ID Electron Microscopy www.sciencedirect.com
  • 4 graph download models