Code

I develop open-source software for neuroanatomy and connectomics, mostly in R as part of the natverse and in Python. The main products are listed below; see my GitHub for the rest.

Brain and nerve cord (BANC) connectome

• bancr — the primary R client for the BANC connectome. GitHub · Zenodo
• influencer — R implementation of the linear-dynamics influence model. GitHub · Zenodo
• ConnectomeInfluenceCalculator — Python influence engine (Drugowitsch lab). GitHub · Zenodo
• nat.ggplot — publication-quality 2D rendering of neurons and meshes. GitHub · Zenodo
• bancpipeline — the R + SLURM pipeline behind the BANC compiled data. GitHub · Zenodo
• BANC-project — analysis code and figures for the BANC paper. GitHub · Zenodo

natverse R packages

• natverse — the meta-package tying the ecosystem together. GitHub
• nat — the core NeuroAnatomy Toolbox for reading, analysing and plotting neurons. GitHub
• neuprintr — query neuPrint connectome servers (e.g. the hemibrain). GitHub
• neuronbridger — work with NeuronBridge light-to-EM neuron matches. GitHub
• neuromorphr — client for NeuroMorpho.org. GitHub
• insectbrainr — client for the Insect Brain Database. GitHub
• mouselightr — work with MouseLight whole-brain mouse neurons. GitHub

Each package’s documentation and tutorials are linked from its GitHub page; several are also written up in my portfolio.