Research, software, and the bits in between.
Open-source tools and the research behind them, from a decade in neuroimaging: distortion correction, brain extraction, surface visualisation, and the developer tooling that keeps regulated software testable.
Projects
Everything on GitHub- 01
warpkit
Python library for neuroimaging transforms and the reference implementation of MEDIC, Multi-Echo DIstortion Correction for fMRI. The phase difference between echoes in every frame becomes a B0 field map, so distortion is corrected as the head moves rather than once from a static field map. Ships as wheels, standalone binaries and a Docker image; the phase-unwrapping core is a C++17 port of ROMEO. Published in Imaging Neuroscience; patent pending.
- 02
wbsurfer2
Command-line tool for turning CIFTI surface data into movies with Connectome Workbench 2. A refresh of the original wbsurfer, distributed as compiled binaries for each OS as well as on PyPI.
- 03
- 04
difftrace
Change detection for uv monorepos. Parses uv.lock into the workspace dependency graph, maps a git diff onto packages, and walks reverse dependencies to find everything transitively affected, so CI only builds, tests and deploys what a change actually touches. Zero runtime dependencies; ships as a GitHub Action.
- 05
brainextractor
FSL's Brain Extraction Tool re-implemented in pure Python: a deformable surface model that finds the brain boundary without the original toolchain.