The choroid, a highly vascular layer behind the retina, is an extension of the central nervous system and has parallels with the renal cortex, with blood flow far exceeding that of the brain and kidney. Thus, there has been growing interest of choroidal blood flow reflecting physiological status of systemic disease. Optical coherence tomography (OCT) enables high-resolution imaging of the choroid, but conventional analysis methods remain manual or semi-automatic, limiting reproducibility, standardisation and clinical utility. In this thesis, I develop several new methods to analyse the choroid in OCT image sequences, with each successive method improving on its predecessors. I first develop two semi-automatic approaches for choroid region (Gaussian Process Edge Tracing, GPET) and vessel (Multi-scale Median Cut Quantisation, MMCQ) analysis, which improve on manual approaches but remain user-dependent. To address this, I introduce DeepGPET, a deep learning-based region segmentation method which improves on execution time, reproducibility, and end-user accessibility, but lacks choroid vessel analysis and automatic feature measurement. Improving on this, I developed Choroidalyzer, a deep learning-based pipeline to segment the choroidal space and vessels and generate fully automatic, clinically meaningful and reproducible choroidal features. I provide rigorous evaluation of these four approaches and consider their potential clinical value in three applications into systemic health: OCTANE, assessing choroidal changes in renal transplant recipients and donors; PREVENT, exploring choroidal associations with Alzheimer's risk factors at mid-life; D-RISCii, assessing choroidal variation and feasibility of OCT in critical care. In short, this thesis contributes many open-source tools for standardised choroidal measurement and highlights the choroid's potential as a biomarker in systemic health.