  The success and generalisation of deep learning algorithms heavily depend on
learning good feature representations. In medical imaging this entails
representing anatomical information, as well as properties related to the
specific imaging setting. Anatomical information is required to perform further
analysis, whereas imaging information is key to disentangle scanner variability
and potential artefacts. The ability to factorise these would allow for
training algorithms only on the relevant information according to the task. To
date, such factorisation has not been attempted. In this paper, we propose a
methodology of latent space factorisation relying on the cycle-consistency
principle. As an example application, we consider cardiac MR segmentation,
where we separate information related to the myocardium from other features
related to imaging and surrounding substructures. We demonstrate the proposed
method's utility in a semi-supervised setting: we use very few labelled images
together with many unlabelled images to train a myocardium segmentation neural
network. Specifically, we achieve comparable performance to fully supervised
networks using a fraction of labelled images in experiments on ACDC and a
dataset from Edinburgh Imaging Facility QMRI. Code will be made available at
https://github.com/agis85/spatial_factorisation.
