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
Nki-enh_0115564_biggraphs brain 1827242 94697307 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0116834_biggraphs brain 1827242 75989524 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0116842_biggraphs brain 1827242 96639233 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0117168_biggraphs brain 1827242 119572073 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0118051_biggraphs brain 1827242 93291452 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0120538_biggraphs brain 1827242 125145539 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0121498_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_0127733_biggraphs brain 1827242 101941698 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0127800_biggraphs brain 1827242 355406333 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0135671_biggraphs brain 1827242 124744560 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0136416_biggraphs brain 1827242 149317394 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0168357_biggraphs brain 1827240 98118700 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Nki-enh_0168413_biggraphs brain 1827240 94829800 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Nki-enh_0171266_biggraphs brain 1827240 80206600 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Nki-enh_0179454_biggraphs brain 1827240 129275000 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Nki-enh_0181535_biggraphs brain 1827240 89754300 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Nki-enh_0181960_biggraphs brain 1827240 67457300 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Nki-enh_0182376_biggraphs brain 1827240 102239000 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Nki-enh_0183726_biggraphs brain 1827240 104511000 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Nki-enh_0185428_biggraphs brain 1827240 104498000 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Nki-enh_0186067_biggraphs brain 1827240 115123000 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Nki-enh_0190053_biggraphs brain 1827240 87035100 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Nki-enh_0190501_biggraphs brain 1827240 70440600 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Nki-enh_0195031_biggraphs brain 1827240 156301000 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Nki-enh_0195236_biggraphs brain 1827240 85174200 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_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