CCM open-source software
The Centre develops open-source tools that integrate imaging, multiscale modelling and machine learning. These software projects form the foundations of our digital-twin pipelines and support collaborative research across UCL and our clinical partners.
Core software projects
Pymira
Python library for reading, editing and writing spatial graph structures.
View on GitHubtUbeNet
Deep learning for vascular structure extraction.
View on GitHubRetinaSim / VesselSim
Multiscale simulation of flow, transport and vascular physiology in realistic networks.
View on GitHubREANIMATE
Imaging informed modelling of tumour microenvironments and therapy response.
View on GitHubOpen access data
RetinaSim
Simulated retina vascular networks (from Brown, E.E., Guy, A.A., Holroyd, N.A. et al. Physics-informed deep generative learning for quantitative assessment of the retina. Nat Commun 15, 6859 (2024). https://doi.org/10.1038/s41467-024-50911-y)
View on GitHubtUbeNet
tUbeNet training data and model weights...
View on GitHubTools, platforms and infrastructure
CCM software is supported by shared development practices, GPU-accelerated compute platforms and common data pipelines used across the Centre. Many of our workflows integrate directly with UCL's HPC ecosystem, the Condenser on-prem cloud and clinical imaging archives.
The Centre maintains shared Python libraries and reference pipelines for graph processing, simulation, deep learning and model validation. These enable reproducibility and accelerate collaboration across projects.
We welcome contributions and external collaborators. Researchers interested in extending TubeNet, VesselSim, REANIMATE or associated tools can contact the CCM software team or open an issue on GitHub.