Project Contacts

For further information about this project, please contact:

• Dr Alistair Poll (alistair.poll@newcastle.ac.uk)
• Dr Dean Thompson (dean.thompson@newcastle.ac.uk)

Project Description

Running batched image analysis and single-cell sequencing pipelines on large biological datasets using parallel and GPU-accelerated HPC workflow

Software or Compute Methods

Python (Cellpose) for GPU-accelerated microscopy image segmentation

Python scientific stack (numpy, pandas, scikit-image) for feature extraction from images

R (tidyverse, flowCore) for flow cytometry processing and statistical analysis

R and Python for downstream data integration, QC, and visualisation

Batch, embarrassingly-parallel jobs over large image and sample sets

Moderate CPU and memory use; GPU required for image segmentation