Projects

This page is non-exhaustive, and lists just a few projects I've worked on.

Featured

AI OnDemand (AIoD)

Lead

A framework for running bioimage analysis models on any compute environment — local, HPC, or cloud — without requiring users to manage installation or scaling.

Python Nextflow Napari HPC Biology Computer Vision
site code

Spherical Phenotype Clustering

Contributor

Contrastive learning approach using experimental metadata as learned class vectors to improve representations

Contrastive Learning Phenotypic Screening Representation Learning
paper

4i Analysis Pipeline

Lead

An end-to-end Nextflow pipeline for tiling, processing, segmenting, and analysing multiplex imaging data.

Nextflow Python Multiplex Imaging

All Projects

HAWKS

Lead

A tool for generating synthetic clustering datasets with controllable difficulty — used to benchmark and stress-test clustering algorithms via evolutionary multi-objective optimisation.

Python Evolutionary Algorithms Clustering Synthetic Data Research
site code paper

Vesicle Segmentation Pipeline

Lead

A Segment Anything–based pipeline for automated vesicle segmentation in cryo-EM micrographs, deployed on our HPC cluster for large data.

Python SAM Cryo-EM HPC

Hole Detection Model

Lead

A deep learning pipeline for automated detection and analysis of holes in time-lapse videos.

Python Deep Learning Image Analysis

Neurotransmitter Classification

Lead

Image classification of synapses and neurons by neurotransmitter type (acetylcholine, GABA, glutamate) from electron micrographs, using a CNN trained in PyTorch.

Python PyTorch Deep Learning Neuroscience HPC