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
Jung2015_m87171241_biggraphs brain 1827240 76259500 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Jung2015_m87171451_biggraphs brain 1827240 225587000 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Jung2015_m87175401_biggraphs brain 1827240 210122000 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Jung2015_m87178158_biggraphs brain 1827240 56143200 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Jung2015_m87179325_biggraphs brain 1827240 83478600 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Jung2015_m87181127_biggraphs brain 1827240 49745600 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Jung2015_m87187287_biggraphs brain 1827240 92434700 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Jung2015_m87190499_biggraphs brain 1827240 183117000 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Jung2015_m87191891_biggraphs brain 1827240 57531200 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Jung2015_m87192457_biggraphs brain 1827240 53436300 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Jung2015_m87195011_biggraphs brain 1827240 205709000 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Jung2015_m87195434_biggraphs brain 1827240 75655800 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Jung2015_m87195645_biggraphs brain 1827240 224526000 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Jung2015_m87196641_biggraphs brain 1827240 65162300 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Jung2015_m87198091_biggraphs brain 1827240 50871300 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Nki-enh_0105488_biggraphs brain 1827242 108555364 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0106057_biggraphs brain 1827242 83501924 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0108355_biggraphs brain 1827242 77976581 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0109727_biggraphs brain 1827242 115995005 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0110809_biggraphs brain 1827242 100117769 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0111282_biggraphs brain 1827242 95295258 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0112249_biggraphs brain 1827242 84188317 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0112347_biggraphs brain 1827242 40239008 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0113013_biggraphs brain 1827242 84683048 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0113044_biggraphs brain 1827242 87622855 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me

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_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_brain_2 brain 91 628 source, region, DOI, sensor name, id SLN_perc, Dist_mm 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
P.pacificus_neural.synaptic_2 neural synaptic 50 611 info, source, region, DOI, sensor name, id synapse.ID Electron Microscopy — www.sciencedirect.com
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
  • 4 graph download models