Connectome Python Packages

navis

Python library for analysis of neuroanatomical data.

fafbseg

Tools to work with the FlyWire connectome. Fully interoperable with navis.

fly-harness

Sparse, model-agnostic harness for deployed biological simulations.

brainfc

Resting-state fMRI functional connectivity, connectome, brain network and hypergraph analysis in Python with a local GUI. 静息态 fMRI · 功能连接矩阵 · 脑网络 · 超图分析

flyconn

Research-grade toolkit over public Drosophila connectomes: harmonized data, signed graphs, uncertainty, validated LIF simulation, declarative experiments

chunkflow

Compose chunk operators to create a pipeline for local or distributed petabyte-scale computation

brain-indexer

Create indexes of simple shapes and find all indexed elements that intersect with a query region.

fly-ftl-extract

Drop-in replacement for ftl-extract where a simulated Drosophila mushroom body (FlyWire connectome, LIF neurons, dopamine-trained readout) decides which strings are Fluent keys. Byte-for-byte the same output. A joke that is literally true.

sparxml

Spiky Neural Networks in Jax

connectomemapper

Connectome Mapper 3 is a BIDS App that implements full anatomical, diffusion, resting/state functional MRI, and recently EEG processing pipelines, from raw T1 / DWI / BOLD , and preprocessed EEG data to multi-resolution brain parcellation with corresponding connection matrices.

dyconnmap

A dynamic connectome mapping module in python.

spacon

SpaCon, a deep-learning method that integrates spatial transcriptomic data with connectomic data to identify functionally relevant brain domains defined by both their molecular makeup and shared connectivity.

neuropull

A (soon to be) lightweight Python package for accessing single-cell connectome networks with metadata.