Fully-supervised deep learning segmentation models are inflexible when encountering new unseen semantic classes and their fine-tuning often requires significant amounts of annotated data. Few-shot semantic segmentation (FSS) aims to solve this inflexibility by learning to segment an arbitrary unseen semantically meaningful class by referring to only a few labeled examples, without involving fine-tuning. State-of-the-art FSS methods are typically designed for segmenting natural images and rely on abundant annotated data of training classes to learn image representations that generalize well to unseen testing classes. However, such a training mechanism is impractical in annotation-scarce medical imaging scenarios. To address this challenge, in this work, we propose a novel self-supervised FSS framework for medical images, named SSL-ALPNet, in order to bypass the requirement for annotations during training. The proposed method exploits superpixel-based pseudo-labels to provide supervision signals. In addition, we propose a simple yet effective adaptive local prototype pooling module which is plugged into the prototype networks to further boost segmentation accuracy. We demonstrate the general applicability of the proposed approach using three different tasks: organ segmentation of abdominal CT and MRI images respectively, and cardiac segmentation of MRI images. The proposed method yields higher Dice scores than conventional FSS methods which require manual annotations for training in our experiments.

Quantification of anatomical shape changes currently relies on scalar global indexes which are largely insensitive to regional or asymmetric modifications. Accurate assessment of pathology-driven anatomical remodeling is a crucial step for the diagnosis and treatment of many conditions. Deep learning approaches have recently achieved wide success in the analysis of medical images, but they lack interpretability in the feature extraction and decision processes. In this work, we propose a new interpretable deep learning model for shape analysis. In particular, we exploit deep generative networks to model a population of anatomical segmentations through a hierarchy of conditional latent variables. At the highest level of this hierarchy, a two-dimensional latent space is simultaneously optimised to discriminate distinct clinical conditions, enabling the direct visualisation of the classification space. Moreover, the anatomical variability encoded by this discriminative latent space can be visualised in the segmentation space thanks to the generative properties of the model, making the classification task transparent. This approach yielded high accuracy in the categorisation of healthy and remodelled left ventricles when tested on unseen segmentations from our own multi-centre dataset as well as in an external validation set, and on hippocampi from healthy controls and patients with Alzheimer's disease when tested on ADNI data. More importantly, it enabled the visualisation in three-dimensions of both global and regional anatomical features which better discriminate between the conditions under exam. The proposed approach scales effectively to large populations, facilitating high-throughput analysis of normal anatomy and pathology in large-scale studies of volumetric imaging.

Deep learning approaches have achieved state-of-the-art performance in cardiac magnetic resonance (CMR) image segmentation. However, most approaches have focused on learning image intensity features for segmentation, whereas the incorporation of anatomical shape priors has received less attention. In this paper, we combine a multi-task deep learning approach with atlas propagation to develop a shape-refined bi-ventricular segmentation pipeline for short-axis CMR volumetric images. The pipeline first employs a fully convolutional network (FCN) that learns segmentation and landmark localization tasks simultaneously. The architecture of the proposed FCN uses a 2.5D representation, thus combining the computational advantage of 2D FCNs networks and the capability of addressing 3D spatial consistency without compromising segmentation accuracy. Moreover, a refinement step is designed to explicitly impose shape prior knowledge and improve segmentation quality. This step is effective for overcoming image artifacts (e.g., due to different breath-hold positions and large slice thickness), which preclude the creation of anatomically meaningful 3D cardiac shapes. The pipeline is fully automated, due to network's ability to infer landmarks, which are then used downstream in the pipeline to initialize atlas propagation. We validate the pipeline on 1831 healthy subjects and 649 subjects with pulmonary hypertension. Extensive numerical experiments on the two datasets demonstrate that our proposed method is robust and capable of producing accurate, high-resolution, and anatomically smooth bi-ventricular 3D models, despite the presence of artifacts in input CMR volumes.

Motivation: Left ventricular (LV) hypertrophy is a strong predictor of cardiovascular outcomes, but its genetic regulation remains largely unexplained. Conventional phenotyping relies on manual calculation of LV mass and wall thickness, but advanced cardiac image analysis presents an opportunity for high-throughput mapping of genotype-phenotype associations in three dimensions (3D). Results: High-resolution cardiac magnetic resonance images were automatically segmented in 1124 healthy volunteers to create a 3D shape model of the heart. Mass univariate regression was used to plot a 3D effect-size map for the association between wall thickness and a set of predictors at each vertex in the mesh. The vertices where a significant effect exists were determined by applying threshold-free cluster enhancement to boost areas of signal with spatial contiguity. Experiments on simulated phenotypic signals and SNP replication show that this approach offers a substantial gain in statistical power for cardiac genotype-phenotype associations while providing good control of the false discovery rate. This framework models the effects of genetic variation throughout the heart and can be automatically applied to large population cohorts. Availability and implementation: The proposed approach has been coded in an R package freely available at https://doi.org/10.5281/zenodo.834610 together with the clinical data used in this work. Contact: [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.