Scientist with a backround in computational biology. Building research tools and reproducible analysis pipelines. Here are some of the projects I've worked on over the years:
Research projects:
- andi_challenge: Analysis of single particle tracking data using CNNs
- 2023-Illukkumbura-JCB: PDE modelling of advective transport
- 2023-Bland: Using image analysis and modelling to study membrane-protein cooperativity
- 202x-Rodrigues (In prep): Statistical analysis of cellular phenotypes
Image analysis tools:
- saibr_fiji_plugin: GUI-based FIJI plugin for performing spectral autofluorescence correction on biological images
- par-segmentation: Unsupervised ML model for segmenting images of cells and quantifying concentration profiles of membrane proteins
- matplotlib-polyroi: Simple tool for selecting polygon/spline ROIs on images using matplotlib/Jupyter
Modelling tools:
- pde-rk: Tool for simulating one-dimensional PDE models with an adaptive Runge-Kutta scheme
- parameter-space-2d: Tool for performing 2D parameter space analysis for deterministic models using parallel processing
Theses:
- PhD thesis: Molecular feedback and self-organisation in the PAR polarity network
- MSci thesis: Computational modelling of Retinotopic Map formation