leaf_analysis_toolkit
PythonScripts for examining leaf image time-series — quantifying growth and shape change across development.
Principal Data Scientist · Cambridge, UK
I turn complex systems
into quantitative answers.
Physicist by training, plant biophysicist by research, data scientist by trade. I spent a decade measuring and modelling how living tissues grow and deform — now I apply the same quantitative instinct to machine learning and healthcare data. The flock drifting behind this text is a live simulation, written from scratch — because I still like to build.
01
Research & publications
Peer-reviewed work in plant biomechanics, morphogenesis and cell-scale imaging — spanning experiment, image analysis and mathematical modelling.
532Citations
10h-index
11i10-index
9Journal articles
Source: Google Scholar
Current Biology · 2017124 cites
Stomatal opening involves polar, not radial, stiffening of guard cells
View paper →Nature Communications · 201998 cites
Nuclear calcium signatures are associated with root development
View paper →The Plant Journal · 201579 cites
Auxin influx importers modulate serration along the leaf margin
View paper →Development · 201762 cites
Pavement cells and the topology puzzle
View paper →Current Biology · 202159 cites
KATANIN and CLASP function at different spatial scales to mediate microtubule response to mechanical stress in Arabidopsis cotyledons
View paper →Current Biology · 202428 cites
Xyloglucan deficiency leads to a reduction in turgor pressure and changes in cell wall properties, affecting early seedling establishment
View paper →PNAS · 202323 cites
Stiffness transitions in new walls post-cell division differ between Marchantia polymorpha gemmae and Arabidopsis thaliana leaves
View paper →Developmental Cell · 202419 cites
Differential growth is an emergent property of mechanochemical feedback mechanisms in curved plant organs
View paper →New Phytologist · 202415 cites
Synthesis and import of GDP‑ʟ‑fucose into the Golgi affect plant–water relations
View paper →Full list, metrics and co-authors on Google Scholar and ResearchGate.
02
Code
Open-source scientific tooling and side projects. Most of the research code below powered the analysis behind the papers above.
JPKforceparse
PythonA parser for JPK atomic-force-microscopy data — the measurement backbone of my cell-mechanics work.
gaussproj
PythonA modified maximum-intensity-projection technique for confocal image stacks, preserving surface detail.
draco_stem
PythonReconstructs 3D meshes from segmented shoot-apical-meristem tissue images (OpenAlea).
wiggler
PythonA tiny cross-platform mouse-wiggler / anti-sleep utility. Small, but
packaged properly with uv.
This site's infrastructure
Self-hostedServed from a Mac in my flat: dnsmasq, a dockerised nginx, a Cloudflare Tunnel, and Cloudflare Access gating private services.
ExperiencePresent
Principal Data Scientist
Camgenium
Machine learning and statistical methods applied to healthcare and diagnostics data.
Experience~2014–2021
Research Associate
Sainsbury Laboratory, University of Cambridge
Computational and quantitative biology: live-cell imaging, image analysis, biomechanics and modelling of plant morphogenesis.
Education2014
PhD, Plant Biophysics
University of Sheffield
In vivo analysis of plant cell mechanics using atomic force microscopy.
Education—
MPhys, Theoretical Physics
University (edit)
Foundation in mathematical and computational modelling.
Skills
Data science & ML
- Python (pandas, NumPy)
- scikit-learn
- Statistics
- Healthcare data
Scientific computing
- Image analysis (scikit-image)
- Biomechanics modelling
- Confocal / AFM data
- Reproducible pipelines
Engineering
- Docker & self-hosting
- PostgreSQL
- Rust
- Linux & infra-as-code
04
Contact
Open to conversations about data science, computational biology, or interesting quantitative problems.