Kristine Aavild Juhl

Xabier Morales, Jordi Mill, Guillem Simeon et al.

The assessment of left atrial appendage (LAA) thrombogenesis has experienced major advances with the adoption of patient-specific computational fluid dynamics (CFD) simulations. Nonetheless, due to the vast computational resources and long execution times required by fluid dynamics solvers, there is an ever-growing body of work aiming to develop surrogate models of fluid flow simulations based on neural networks. The present study builds on this foundation by developing a deep learning (DL) framework capable of predicting the endothelial cell activation potential (ECAP), linked to the risk of thrombosis, solely from the patient-specific LAA geometry. To this end, we leveraged recent advancements in Geometric DL, which seamlessly extend the unparalleled potential of convolutional neural networks (CNN), to non-Euclidean data such as meshes. The model was trained with a dataset combining 202 synthetic and 54 real LAA, predicting the ECAP distributions instantaneously, with an average mean absolute error of 0.563. Moreover, the resulting framework manages to predict the anatomical features related to higher ECAP values even when trained exclusively on synthetic cases.

Josefine Vilsbøll Sundgaard, Kristine Aavild Juhl, Jakob Mølkjær Slipsager

This paper presents our contribution to the REFUGE challenge 2020. The challenge consisted of three tasks based on a dataset of retinal images: Segmentation of optic disc and cup, classification of glaucoma, and localization of fovea. We propose employing convolutional neural networks for all three tasks. Segmentation is performed using a U-Net, classification is performed by a pre-trained InceptionV3 network, and fovea detection is performed by employing stacked hour-glass for heatmap prediction. The challenge dataset contains images from three different data sources. To enhance performance, cycleGANs were utilized to create a domain-shift between the data sources. These cycleGANs move images across domains, thus creating artificial images which can be used for training.

Kristine Aavild Juhl, Jakob Slipsager, Ole de Backer et al.

Patients with atrial fibrillation have a 5-7 fold increased risk of having an ischemic stroke. In these cases, the most common site of thrombus localization is inside the left atrial appendage (LAA) and studies have shown a correlation between the LAA shape and the risk of ischemic stroke. These studies make use of manual measurement and qualitative assessment of shape and are therefore prone to large inter-observer discrepancies, which may explain the contradictions between the conclusions in different studies. We argue that quantitative shape descriptors are necessary to robustly characterize LAA morphology and relate to other functional parameters and stroke risk. Deep Learning methods are becoming standardly available for segmenting cardiovascular structures from high resolution images such as computed tomography (CT), but only few have been tested for LAA segmentation. Furthermore, the majority of segmentation algorithms produces non-smooth 3D models that are not ideal for further processing, such as statistical shape analysis or computational fluid modelling. In this paper we present a fully automatic pipeline for image segmentation, mesh model creation and statistical shape modelling of the LAA. The LAA anatomy is implicitly represented as a signed distance field (SDF), which is directly regressed from the CT image using Deep Learning. The SDF is further used for registering the LAA shapes to a common template and build a statistical shape model (SSM). Based on 106 automatically segmented LAAs, the built SSM reveals that the LAA shape can be quantified using approximately 5 PCA modes and allows the identification of two distinct shape clusters corresponding to the so-called chicken-wing and non-chicken-wing morphologies.