Fly Brain HubHemibrain
HHMI Janelia Research Campus (FlyEM Project Team)
Dense synaptic-level reconstruction of a large part of the central fly brain, including the mushroom body and central complex, produced by Janelia's FlyEM team. It contains roughly 25,000 neurons sorted into thousands of cell types, with v1.0 released in January 2020 and v1.2 in December 2020. The overview paper was published in eLife and the data is served through neuPrint.
Sources checked
Every fact above was read from these pages on the date the entry was added.
- janelia.org https://www.janelia.org/project-team/flyem/hemibrain
Used by: 10 projects
NAVis
navis-org (Fly Connectomics group, Cambridge)
A general-purpose Python library for handling neuron skeletons, meshes, dotprops and image volumes, with 2D/3D plotting, morphometrics, NBLAST similarity and template-brain transforms built in. Developed in the Cambridge fly connectomics community as the Python counterpart of the R natverse, it plugs into neuPrint and, through the fafbseg extension, FlyWire/FAFB. Performance-critical pieces have been moved to Rust via navis-fastcore.
connectome_interpreter
Yijie Yin, University of Cambridge
A Python library that turns a wiring diagram into testable hypotheses about circuit function, and it runs on a laptop or in Colab even for whole-brain analyses of around 140,000 neurons. It computes polysynaptic effective connectivity between groups of neurons with or without signs, retrieves and plots the actual subcircuit between sources and targets, and exposes a differentiable connectome model. Installable from PyPI, with an accompanying preprint and Colab notebook.
coconatfly
Gregory Jefferis (natverse)
An R package from Greg Jefferis that puts one uniform interface over the major fly connectomes so the same partner-query or cell-type comparison can be run across hemibrain, FlyWire, MANC, FANC, BANC, the male CNS and the male optic lobe. It is flagged as experimental and its API may still change, but it is already the workhorse for hemibrain-versus-FlyWire comparisons in the natverse community.
connectome_data_prep
Yijie Yin, University of Cambridge
Yijie Yin's (Cambridge) notebooks and scripts for turning raw connectome releases into analysis-ready sparse connectivity matrices and metadata tables, with axon/dendrite splitting via flow centrality. It covers the adult male CNS, BANC, FlyWire/FAFB, hemibrain and MANC as well as the larval connectome, and includes benchmarking code for the pathfinding and effective-connectivity analyses used in the Connectome Interpreter framework. No license file is present.
Fly Connectome Data Tutorial (SJCABS)
SJCABS winter school (Sven Dorkenwald & Alexander Bates)
Course material from the San Juan Winter School on Connectomics and Brain Simulation, written by Sven Dorkenwald and Alexander Bates, that walks students from loading data to morphology, direct and indirect connectivity analysis in both Python and R. Its most useful feature is a harmonised metadata schema and a public cloud bucket covering BANC, FAFB, the male CNS, MANC and hemibrain, so the same notebooks run across all five datasets.
natverse / nat
Jefferis lab, MRC LMB
A tidyverse-style family of interoperable R packages for importing, visualising, analysing and exporting 3D neuroanatomy, built around the core nat (NeuroAnatomy Toolbox) package that Greg Jefferis's group has maintained on GitHub since 2014. Satellite packages such as neuprintr and fafbseg give R users access to hemibrain and FlyWire/FAFB data. The ecosystem was described by Bates, Jefferis and colleagues in eLife in 2020.
neuPrint
Janelia FlyEM (HHMI)
Janelia's connectome analysis ecosystem: a Neo4j-backed graph database plus the neuPrintExplorer web front end and an HTTP API for querying neurons and synaptic connectivity. It is the official home of the hemibrain, MANC and male CNS datasets from the FlyEM team, and the ecosystem was described in a 2022 Frontiers in Neuroinformatics paper by Plaza et al.
neuprint-python
Janelia FlyEM (HHMI)
The official Python client for the neuPrint service, letting you pull neuron metadata, connectivity tables and skeletons from Janelia's connectome databases into pandas without writing Cypher by hand. First published on PyPI in January 2020 and still actively released (0.6.3 in July 2026), it is installable via pip, conda or pixi.
Virtual Fly Brain
Virtual Fly Brain consortium (UK institutions incl. MRC HGU)
A long-running UK-funded web atlas that registers neuron images, gene-expression patterns and connectomics onto standard Drosophila brain templates and links them through an anatomy ontology, so anatomy, expression and connectivity can be cross-searched in one place. Supported since 2009, it now indexes over 600,000 3D images and roughly 490,000 neurons with connectivity, spanning hemibrain, FlyWire, FANC and the larval L1EM data. The v2 front end (geppetto-vfb) is an MIT-licensed customisation of the Geppetto platform.
Wikipedia: Drosophila connectome
Wikipedia (Wikimedia Foundation)
Community-written encyclopedia article that serves as a one-stop overview of fruit fly connectomics, explaining why Drosophila is used as a model and walking through the major datasets from the 3,016-neuron larval brain to the adult hemibrain, FlyWire, the FANC and MANC nerve cords, and the 2025 whole-CNS BANC and male CNS reconstructions. It also touches on how wiring structure relates to behavior. Text is under CC BY-SA 4.0; last edited August 11, 2026.