Wellcome / EPSRC Centre for Interventional and Surgical Sciences


WEISS Open Source Tools


LogoDescriptionWebsiteDocsCodeLead DeveloperRef
Scikit-surgery logo
SciKit-Surgery libraries implements a family of compact, orthogonal, libraries accompanied by robust testing, documentation, and quality control. SciKit-Surgery libraries can be rapidly assembled into testable clinical applications and subsequently translated to production software without the need for software reimplementation.scikit-surgery.orgDocsSourceDr. Matt Clarkson[1] [2] [3]
Deep Reg logo
DeepReg is a freely available, community-supported open-source toolkit for research and education in medical image registration using deep learning.deepreg.netDocsSourceDr. Yipeng Hu[4]
TorchIO logo
Medical image preprocessing and augmentation toolkit for deep learning. Docs


Fernando Pérez-García[5]
Semiology visualisation logo
Epilepsy Seizure Semiology-to-Brain Visualisation Tool (SVT) - v 1.7.1. DocsSourceDr Ali Alim-Marvasti[draft]
Affine pose graph optimisation based on G2O framework DocsGithubDr. Liang Li[draft]
Resector is an Implementation of a TorchIO transform used to simulate a resection cavity from a T1-weighted brain MRI and a corresponding geodesic information flows (GIF) brain parcellation (version 3.0). [Preprint on arXiv]  SourceFernando Pérez-García[6]
Integrated multi-modality image-guided navigation for neurosurgery
Integrated intraoperative navigation system is tailored to skull base neurosurgery with the ability to incorporate (1) preoperative structural MR and CT imaging and 3D volume reconstructions of the tumour and surrounding anatomy (e.g. facial nerve), (2) neurophysiological monitoring and stimulation and (3) live reconstructed 3D ultrasound. [ref]  SourceDr. Jonathan Shapey[7]



  1. Thompson, S., Dowrick, T., Ahmad, M., Xiao, G., Koo, B., Bonmati, E., Kahl, K. and Clarkson, M.J., 2020. SciKit-Surgery: compact libraries for surgical navigation. International Journal of Computer Assisted Radiology and Surgery. DOI: 10.1007/s11548-020-02180-5
  2. Thompson, S., Dowrick, T., Xiao, G., Ramalhinho, J., Robu, M., Ahmad, M., Taylor, D. and Clarkson, M.J., 2020. SnappySonic: An Ultrasound Acquisition Replay Simulator. Journal of open research software, 8(1). DOI: 10.5334/jors.289
  3. Thompson, S; Dowrick, T; Ahmad, M; Opie, J; Clarkson, M; (2021) Are fiducial registration error and target registration error correlated? SciKit-SurgeryFRED for teaching and research. In: (Proceedings) SPIE Medical Imaging Image-Guided Procedures, Robotic Interventions, and Modeling. SPIE (In press). https://discovery.ucl.ac.uk/id/eprint/10112339/
  4. Fu, Y., Brown, N.M., Saeed, S.U., Casamitjana, A., Baum, Z., Delaunay, R., Yang, Q., Grimwood, A., Min, Z., Blumberg, S.B. and Iglesias, J.E., 2020. DeepReg: a deep learning toolkit for medical image registration. arXiv preprint arXiv:2011.02580. https://joss.theoj.org/papers/10.21105/joss.02705
  5. Pérez-García, F., Sparks, R. and Ourselin, S., 2020. TorchIO: a Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning. arXiv preprint arXiv:2003.04696. https://arxiv.org/abs/2003.04696
  6. Pérez-García, F., Rodionov, R., Alim-Marvasti, A., Sparks, R., Duncan, J.S. and Ourselin, S., 2020, October. Simulation of brain resection for cavity segmentation using self-supervised and semi-supervised learning. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 115-125). Springer, Cham. https://arxiv.org/pdf/2006.15693.pdf 
  7. Shapey, J., Dowrick, T., Delaunay, R. et al. Integrated multi-modality image-guided navigation for neurosurgery: open-source software platform using state-of-the-art clinical hardware. Int J CARS (2021). https://doi.org/10.1007/s11548-021-02374-5