Machine learning has emerged as a crucial tool for medical image analysis, largely due to recent developments in deep artificial neural networks addressing numerous, diverse clinical problems. As with any conceptual tool, the effective use of machine learning should be predicated on an understanding of its underlying motivations just as much as algorithms or theory — and to do so, we need to explore its philosophical foundations. One of these foundations is the understanding of how values, despite being non-empirical, nevertheless affect scientific research. This article has three goals: to introduce the reader to values in a way that is specific to medical image analysis; to characterise a particular set of technical decisions (what we call the end-to-end vs. separable learning spectrum ) that are fundamental to machine learning for medical image analysis; and to create a simple and structured method to show how these values can be rigorously connected to these technical decisions. This better understanding of how the philosophy of science can clarify fundamental elements of how medical image analysis research is performed and can be improved. • Research values indirectly but fundamentally affect technical decisions in machine learning for medical image analysis. • Machine learning frameworks can be characterised on a spectrum regarding how much they use explicit intermediate representations, i.e. sub-problems. • Structured approaches to values can show what motivates research towards either end of said spectrum.

Medical questionnaires are a valuable source of information but are often difficult to analyse due to both their size and the high possibility of them having missing values. This is a problematic issue in biomedical data science as it may complicate how individual questionnaire data is represented for statistical or machine learning analysis. In this paper, we propose a deeply-learnt residual autoencoder to simultaneously perform non-linear data imputation and dimensionality reduction. We present an extensive analysis of the dynamics of the performance of this autoencoder regarding the compression rate and the proportion of missing values. This method is evaluated on motor and non-motor clinical questionnaires of the Parkinson's Progression Markers Initiative (PPMI) database and consistently outperforms linear coupled imputation and reduction approaches.

Sensitivity to phase deviations in MRI forms the basis of a variety of techniques, including magnetic susceptibility weighted imaging and chemical shift imaging. Current phase processing techniques fall into two families: those which process the complex image data with magnitude and phase coupled, and phase unwrapping-based techniques that first linearize the phase topology across the image. However, issues, such as low signal and the existence of phase poles, can lead both methods to experience error. Cyclic continuous max-flow (CCMF) phase processing uses primal-dual-variational optimization over a cylindrical manifold, which represent the inherent topology of phase images, increasing its robustness to these issues. CCMF represents a third distinct paradigm in phase processing, being the only technique equipped with the inherent topology of phase. CCMF is robust and efficient with at least comparable accuracy as the prior paradigms.

The primary purpose of medical image visualization is to improve patient outcomes by facilitating the inspection, analysis, and interpretation of patient data. This is only possible if the users’ perceptual and cognitive limitations are taken into account during every step of design, implementation, and evaluation of interactive displays. Visualization of medical images, if executed effectively and efficiently, can empower physicians to explore patient data rapidly and accurately with minimal cognitive effort. This article describes a specific case study in biomedical visualization system design and evaluation, which is the visualization of MR angiography images for planning arteriovenous malformation (AVM) interventions. The success of an AVM intervention greatly depends on the surgeon gaining a full understanding of the anatomy of the malformation and its surrounding structures. Accordingly, the purpose of this study was to investigate the usability of visualization modalities involving contour enhancement and stereopsis in the identification and localization of vascular structures using objective user studies. Our preliminary results indicate that contour enhancement, particularly when combined with stereopsis, results in improved performance enhancement of the perception of connectivity and relative depth between different structures.