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_0115824_biggraphs brain 1827242 79151201 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0116039_biggraphs brain 1827242 120915968 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0116065_biggraphs brain 1827242 125848670 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0116415_biggraphs brain 1827242 59943333 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_0118439_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_0119866_biggraphs brain 1827242 143576209 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_0120557_biggraphs brain 1827242 428349317 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0120652_biggraphs brain 1827242 116466312 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_0122169_biggraphs brain 1827242 81351117 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0122512_biggraphs brain 1827242 83237991 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0122816_biggraphs brain 1827242 73156355 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0122844_biggraphs brain 1827242 132950282 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0123173_biggraphs brain 1827242 62109556 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0123429_biggraphs brain 1827242 116714901 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0123657_biggraphs brain 1827242 97735945 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0125762_biggraphs brain 1827242 100686899 source, region, DOI, sensor, Atlas_MNI152_T1_1mm_brain_incremented_index spatial_id, id weight Magnetic Resonance — openconnecto.me
Nki-enh_0126919_biggraphs brain 1827242 91889062 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

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_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
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 — — —
  • 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_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
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
  • 4 graph download models