UKBOB: Large-Scale Segmentator on UK Biobank Dataset

I am a PhD student working in computer vision, with a focus on 3D vision, medical imaging, and geometry. My research interests span several cutting-edge topics, including the application of transformers, optimization techniques, domain gap analysis, and uncertainty quantification. I am keen in driving innovation in computational imaging and machine learning.
Netdevices, Paris
Development of an Application to Automatise Healthcare in Hospitals in France - -
Improvement of a data management tool using AI, automated counting of available hospital beds, and available materials.
Michael Hausser Lab, University College London
Development of virtual reality models for spatial navigation understanding - -
Develop virtual reality (VR) models involving mice training on wheel setup with 2P-microscopy recording. Python-based project to analyse mouse brain activity.
Hugo Spiers Lab, University College London
Spatial Navigation App for Dementia Detection - -
Design and conduction of real-world experiments to validate the spatial navigation game Sea Hero Quest.
UKBOB: Large-Scale Segmentator on UK Biobank Dataset
3D Spine Shape Reconstruction from Single 2D DXA
X-Diffusion : Cross-sectional Diffusion Model for 3D Volume Reconstruction from Single/Few Views
3D Spine Shape Analysis
Automated Scoliosis Measurement on 2D DXA scans from UK Biobank
University of Oxford
DPhil in Engineering, SABS CDT Program - -
Imperial College London
MSc Computational Neuroscience - -
University College London
BSc Mathematics/Statistics & Neuroscience - -
UKBOB: Large-Scale Segmentator on UK Biobank Dataset
Documentation Coming Soon.
3D Spine Shape Estimation from Single 2D DXA
Scoliosis is currently assessed solely on 2D lateral deviations, but recent studies have also revealed the importance of other imaging planes in understanding the deformation of the spine. Consequently, exctracting the spinal geometry in 3D would help quantify these spinal deformations and aid diagnosis. In this study, we propose an automated general framework to estimate the 3D spine shape from 2D DXA scans. We achieve this by explicitly predicting the sagittal view of the spine from the DXA scan. Using these two orthogonal projections of the spine (coronal in DXA, and sagittal from the prediction), we are able to describe the 3D shape of the spine. The prediction is learnt from over 30k paired images of DXA and MRI scans. We assess the performance of the method on a held out test set, and achieve high accuracy. For more information, visit our website : Project Link
X-Diffusion: 3D MRI Volumes Generation
We present X-Diffusion, a cross-sectional diffusion model tailored for Magnetic Resonance Imaging (MRI) data. X- Diffusion is capable of generating the entire MRI volume from just a single MRI slice or optionally from few multiple slices, setting new benchmarks in the precision of synthesized MRIs from extremely sparse observations. The uniqueness lies in the novel view-conditional training and inference of X-Diffusion on MRI volumes, allowing for generalized MRIlearning. The generated MRIs retain essential features of the original MRI, including tumour profiles, spine curvature, brain volume, and beyond. For more information, visit our website : Project Link
3D Shape Analysis of Scoliosis
Scoliosis is typically measured in 2D in the coronal plane, although it is a three-dimensional (3D) condition. Our objective in this work is to analyse the 3D geometry of the spine and its relationship to the vertebral canal. To this end, we make three contributions: first, we extract the 3D space curve of the spine automatically from low-resolution whole-body Dixon MRIs and obtain coronal, sagittal and axial projections for various degrees of scoliosis; second, we also extract the vertebral canal as a 3D curve from the MRIs, and examine the relationship between the two 3D curves; and third, we measure the angle of rotation of the spine and examine the correlation between this 3D measurement and the 2D curvature of the coronal projection. For this study, we use 48,384 MRIs from the UK Biobank.
Project title
We propose improvements to an automated method for scoliosis measurement. Our main novelty is the use of a spline to better model the curve of the spine, and we employ pseudo- labelling to re-train the segmentation step to mitigate the domain gap when adapting to a new dataset. We obtain promising results with a good fit of our smoothed curve to approximate the spinal midpoints in severe scoliosis cases, and obtain good agreement against human ground-truth. This work is relevant for improving the severity grading of scoliosis and potentially aiding in the treatment management of scoliosis.
Project title
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.