ConnectomeKG -- Connectomes as Knowledge Graphs

ConnectomeKG turns an electron-microscopy connectome into a queryable knowledge graph: every neuron a node, every edge a counted synapse, with the cell types, neuropils and community labels layered on top.

The whole fly brain, and where its signal goes. Each sphere is one of the 79 neuropils, sized by its synapse count and colored by brain region, and each tube is one of the 100 strongest flows between them. The gray dots are the cell bodies of all 139,255 neurons. Reading the images explains every mark, and connkg quilt --view flow --floor --cloud --still draws it.

Render of the FlyWire FAFB v783 connectome (Dorkenwald et al. 2024; Schlegel et al. 2024), CC BY-NC-SA 4.0. The image is an adaptation shared under the same license, not under the software's Elastic License 2.0.

Author: Eric G. Suchanek, PhD -- Flux-Frontiers, Liberty TWP, OH

Status: pre-alpha (0.8.1). Three real connectomes build and answer queries, and the 2-D and 3-D views work. The neuPrint reader (hemibrain) and the leaky integrate-and-fire (LIF) what-if simulation are not done yet.

Install

ConnectomeKG needs Python 3.12 or 3.13.

pip install connectome-kg

Add an extra for the parts you want:

For example, pip install "connectome-kg[semantic,viz3d]". To work on the code, clone the repository and run poetry install --with dev --extras semantic, then prefix each command with poetry run.

Quickstart

The quickstart needs no download. connkg fixture writes a 1,000-neuron synthetic connectome shaped like FAFB v783, with three circuits planted in it: feeding (GRN_sugar and GRN_bitter to MN9), escape (LC4 and LPLC2 to DNp01) and grooming (JO-CE to aDN1).

Build a synthetic connectome

1. Write the synthetic connectome:

   connkg fixture --out /tmp/synth1k
   

   wrote synthetic Codex release to /tmp/synth1k
   

2. Build the graph. The build takes about a second.

   connkg --root /tmp/kg --dataset synthetic1k build --data-dir /tmp/synth1k --no-index
   

   ...
   nodes       : 1373  {'cell_type': 154, ..., 'neuron': 1000, 'neuropil': 33, ...}
   edges       : 20242  {..., 'SYNAPSES_TO': 12145, 'TYPE_SYNAPSES_TO': 2198, ...}
   

Ask questions

With one graph under /tmp/kg, the commands find it without --dataset.

What is the strongest route from sugar-sensing neurons to the proboscis motor neuron?

connkg --root /tmp/kg path --from GRN_sugar --to MN9

strength 0.04189, net sign +1
  GRN_sugar/R/720575940473189481
  -> SEZ_IN1/L/720575940473189248  (39 syn, 14.8% of input, sign +1)
  -> MN9/R/720575940473189669  (76 syn, 28.4% of input, sign +1)

Each hop reports its synapse count, its share of the receiving neuron's input, and its transmitter sign.

Does the bitter pathway excite or inhibit the same motor neuron?

connkg --root /tmp/kg path --from GRN_bitter --to MN9

strength 0.02383, net sign -1
  GRN_bitter/R/720575940473189487
  -> SEZ_INb/L/720575940473189251  (29 syn, 21.8% of input, sign +1)
  -> MN9/L/720575940473189668  (33 syn, 10.9% of input, sign -1)

The last hop is inhibitory, so the route has a net sign of -1.

What feeds MN9 through strong connections?

connkg --root /tmp/kg cone MN9 --direction up --min-syn 20

hop 0: 2 neurons
  MN9/L/720575940473189668
  MN9/R/720575940473189669
hop 1: 5 neurons
  AN007/R/720575940473189650
  SEZ_IN1/L/720575940473189248
  SEZ_IN1/L/720575940473189250
  SEZ_IN1/R/720575940473189249
  SEZ_INb/L/720575940473189251

How much of MN9's input does GRN_sugar account for, over every route?

connkg --root /tmp/kg influence --from GRN_sugar --to MN9 --hops 2 --limit 3

influence of GRN_sugar (6 neurons), signed, as a share of the receiving neuron's input

onto MN9 (2 neurons), averaged:
  hop 1: +0.0000
  hop 2: +0.4811
  total: +0.4811
...

The sugar neurons reach MN9 only through a relay, and they account for about 48% of its input two hops out.

What does the whole graph look like?

connkg --root /tmp/kg analyze > report.md

report.md lists node and edge counts, hub neurons, the strongest type-to-type links and neuropil coverage.

Real connectomes

Three releases from the Codex portal build the same way, each into its own graph:

The Codex portal needs a Google sign-in, so you download the files yourself. Get the data lists the files each release needs and how to check them.

To build a release, name it with --dataset. --root and --dataset are global options, so they go before the command:

connkg verify --data-dir fafb_v783
connkg --root . --dataset fafb783 build --data-dir fafb_v783
connkg --root . --dataset banc888 build --data-dir banc_v888

The FAFB v783 build takes about three minutes and 7.2 GB of memory, and writes a 2.3 GB graph. connkg datasets lists the graphs built under a root. When a root holds more than one, every command needs --dataset:

connkg --root . --dataset banc888 cone DNp01 --min-syn 5

Examples

The examples below use the FAFB v783 graph. connkg specs lists every way to name neurons, and connkg <command> --help lists every option.

Ask wiring questions

Find the strongest signed path from the looming detectors to the giant fiber:

connkg --root . --dataset fafb783 path --from LPLC2 --to DNp01

List everything one hop upstream of the giant fiber, keeping connections of 10 synapses or more:

connkg --root . --dataset fafb783 cone DNp01 --direction up --min-syn 10

Rank the cell types that LC4 drives most, over three hops:

connkg --root . --dataset fafb783 influence --from LC4

Open LC4 and DNp01 as FlyWire meshes in the browser, with no login:

connkg --root . --dataset fafb783 link LC4 DNp01

Draw 3-D views

These commands need the viz3d extra. Fetch the neuropil surfaces once first:

connkg --root . --dataset fafb783 meshes

Render the escape circuit inside the brain as a single 4K image:

connkg --root . --dataset fafb783 quilt LPLC2 DNp01 --tubes --cloud --still

Open a query's answer in the interactive viewer, colored hop by hop:

connkg --root . --dataset fafb783 viz3d "path:LPLC2>DNp01"

Open the signal flow through BANC's brain and nerve cord. The viewer's Dataset box switches to any other connectome built under the root, and its View box switches between the circuit and flow views:

connkg --root . --dataset banc888 viz3d --view flow

Leave out --still to render a Looking Glass quilt instead. The circuit view draws each neuron's traced skeleton, which comes from a separate 31 GB download; connkg skeletons caches it once. Rendering the connectome in 3-D covers both views, the viewer and the skeleton cache.

Use the Python API

ConnectomeKG takes the same specs as the CLI. This example opens the quickstart graph:

from connectomekg import ConnectomeKG

with ConnectomeKG("/tmp/kg/connectomes/synthetic1k") as kg:
    path = kg.strongest_path("GRN_sugar", "MN9")
    print(path.strength, path.net_sign)
    for partner in kg.type_partners("DNp01", direction="up", limit=3):
        print(partner)

0.04189280868385347 1
{'cell_type': 'LC4', 'syn_count': 239, 'n_pairs': 16, 'nt_type': 'ACH'}
{'cell_type': 'LPLC2', 'syn_count': 221, 'n_pairs': 20, 'nt_type': 'ACH'}
{'cell_type': 'SN001', 'syn_count': 53, 'n_pairs': 4, 'nt_type': 'ACH'}

kg.cone, kg.influence and kg.neurons_of work the same way.

Serve the graph to an AI agent

connkg-mcp serves the graph over the Model Context Protocol (MCP), so an agent such as Claude Code can call strongest_path, cone, influence and the other queries as tools. Add an entry to your project's .mcp.json:

{
  "mcpServers": {
    "connkg": {
      "command": "connkg-mcp",
      "args": ["--root", "/path/to/connectome_kg", "--dataset", "fafb783"]
    }
  }
}

The command reference lists every tool and its argument limits.

The graph also federates with the rest of the KGRAG fleet: pip install "kg-rag[connectome]".

Documentation

The full documentation is at flux-frontiers.github.io/connectome_kg.

Data and licensing

Each connectome keeps its own license, and a graph built from it is a derived work under the same license:

• FlyWire FAFB v783 is CC BY-NC-SA 4.0: free for non-commercial use only. Keep FAFB graphs out of anything commercial.
• BANC v888 and FlyEM Male CNS v1.0 are CC BY 4.0, which allows commercial use with attribution.

Keep the downloads and the built graphs (connectomes/*/.connectomekg/*.sqlite) out of the repository. .gitignore already excludes them.

The Codex portal tracks the live FlyWire database, so its FAFB files drift from the October 2024 published release. For a reproducible build, use the static snapshots listed in Get the data and record which one you used.

If you use the data, cite the data papers.

FlyWire FAFB v783:

• Dorkenwald, S. et al. (2024). Neuronal wiring diagram of an adult brain. Nature 634, 124-138.
• Schlegel, P. et al. (2024). Whole-brain annotation and multi-connectome cell typing of Drosophila. Nature 634, 139-152.
• Eckstein, N. et al. (2024). Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila melanogaster. Cell 187, 2574-2594.

BANC v888:

• Bates, A. S. et al. (2026). Nature. doi:10.1038/s41586-026-10735-w
• The BANC data deposit: doi:10.7910/DVN/7WTH1N

FlyEM Male CNS v1.0:

• The Male CNS connectome paper, bioRxiv: doi:10.1101/2025.10.09.680999

Citation

If you use ConnectomeKG in research or a project, please cite it. Each GitHub release is archived on Zenodo, and the DOI 10.5281/zenodo.22817369 always resolves to the newest version.

APA

Suchanek, E. G. (2026). ConnectomeKG: Connectomes as Knowledge Graphs (Version 0.8.1) [Software]. Flux-Frontiers. https://doi.org/10.5281/zenodo.22817369

BibTeX

@software{suchanek_connectome_kg,
  author    = {Suchanek, Eric G.},
  title     = {{ConnectomeKG}: Connectomes as Knowledge Graphs},
  version   = {0.8.1},
  year      = {2026},
  publisher = {Flux-Frontiers},
  doi       = {10.5281/zenodo.22817369},
  url       = {https://github.com/Flux-Frontiers/connectome_kg},
}

License

Elastic License 2.0: free for non-commercial and internal use; commercial redistribution or hosting requires a license from Flux-Frontiers. The license covers the software only. The connectome data keeps its own license, described in Data and licensing.

Support

• Issues: GitHub Issues
• Sister projects: ConnectomeKG is part of the KGRAG family of knowledge graphs, with PyCodeKG (Python code), DocKG (documents), MetaboKG (metabolic pathways), GenealogyKG (family history), DiaryKG (journals) and AgentKG (conversational memory).
• Built on: kgmodule-utils, SQLite, sqlite-vec, pandas, SciPy and Click.