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_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_0130249_biggraphs brain 1827242 71227500 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0131127_biggraphs brain 1827242 74151030 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0131832_biggraphs brain 1827242 70715044 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0132088_biggraphs brain 1827242 103073904 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0132717_biggraphs brain 1827242 106926453 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0132850_biggraphs brain 1827242 63673501 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0132995_biggraphs brain 1827242 80077330 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0133436_biggraphs brain 1827242 100361577 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0133894_biggraphs brain 1827242 127128483 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0134795_biggraphs brain 1827242 125457167 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_0136018_biggraphs brain 1827242 115933956 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0136303_biggraphs brain 1827242 75553490 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
Kki2009_113_1_bg brain 1827240 48522300 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Kki2009_113_2_bg brain 1827240 50384100 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Kki2009_127_2_bg brain 1827240 35170000 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Kki2009_142_1_bg brain 1827240 38654900 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Kki2009_142_2_bg brain 1827240 40036000 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Kki2009_239_1_bg brain 1827240 37152600 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Kki2009_239_2_bg brain 1827240 35899100 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Kki2009_346_1_bg brain 1827240 57507200 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Kki2009_346_2_bg brain 1827240 56635100 DOI, ecount, vcount, region, source, Atlas_MNI152_T1_1mm_brain_incremented_index, sensor spatial_id weight Magnetic Resonance — openconnecto.me
Kki2009_422_1_bg brain 1827240 39554400 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_interareal.cortical.network_2 interareal cortical network 93 2667 source, region, DOI, sensor name, id weight 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_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
  • 4 graph download models

Mouse

Download url region # Nodes # Edges Graph Attrs Node Attrs Edge Attrs sensor project Source host url
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_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_visual.cortex_2 cerebral cortex 195 214 info, DOI, region, source, key, sensor type1, id, type2 weight Electron microscopy — www.nature.com
Mouse_visual.cortex_1 cerebral cortex 29 44 info, source, region, DOI, 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.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
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_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