flywire-network-analysis

This repository contains analysis scripts for the network analyses of the Flywire connectome.

Network Paper Preprint: Lin, Yang et al. 2023, "Network Statistics of the Whole-Brain Connectome of Drosophila" (https://www.biorxiv.org/content/10.1101/2023.07.29.551086v2)

Data Paper Preprint: Dorkenwald et al. 2023, "Neuronal wiring diagram of an adult brain" (https://www.biorxiv.org/content/10.1101/2023.06.27.546656v2)

Data exports of the Flywire connectome are hosted at https://codex.flywire.ai/api/download. The analyses in the paper were conducted with the v630 snapshot of the Flywire connectome.

Some Python scripts employ the graphtool package, which only runs on Linux/Mac architectures. Many scripts were run on computational cluster due to the large memory requirements.

Python Scripts

• FlywireAnalysis/v630-Animal-Comparison.ipynb: network definition, synapse and degree distributions, strong and weak connected component analyses, edge percolation, edge reciprocity, clustering coefficient, shortest path, small-world-ness
• FlywireAnalysis/v630-Motif-Analysis.ipynb: Motif frequency and strengh distributions
• FlywireAnalysis/v630-Proximity-Model.ipynb: Connectivity vs. distance distribution and neuron-neuron distance (NND) model: connection probability vs neuron pair arbor distance
• FlywireAnalysis/v630-Rich-Club.ipynb: Rich-club analysis with a configuration (CFG) model and a neuropil connection (NPC) null model
• FlywireAnalysis/v630-Spectral-Properties.ipynb: Random walk and spectral properties
• FlywireAnalysis/v630-Animal-Comparison.ipynb: Compute and network statistics across existing wiring diagrams from different animals
• Rank_analysis.ipynb: relative rank of rich club neuron populations to different sensory inputs, scatterplots comparing relative rank to multiple modalities
• reciprocal_space.ipynb: inter-neuropil neciprocal projectome matrices
• utils & flywireconnectome_utils contain secondary scripts called in the Python notebooks.

MatLab Scripts

• flywire_analyses_codex.m: fractional neuropil projectomes, internal and external neuropil fractions, neuropil fractions by putative neurotransmitter
• flywire_reciprocal_connectivity.m: degree scatterplots, distributions of reciprocal connections and reciprocal degree, reciprocity by neurotransmitter, relative reciprocal degree heatmaps, neuropil-specific highly reciprocal neurons, identifying integrators and broadcasters, characterize properties (cell type, neurotransmitter, etc) of integrators, broadcasters, and rich club neurons.

Data Products

This folder contains data outputs not found on Codex, including the color pallettes used for neuropils, neurotransmitters, and cell types, neuron root_ID lists for various neuron populations, the root_ID list of all reciprocal pairs in v630, and the ranks of neurons from sensory inputs.

Credits

Albert Lin, Runzhe Yang, Sven Dorkenwald

Codex data exports generated by Arie Matsliah