Deep Conditional Shape Models for 3D cardiac image segmentation

Abstract: Delineation of anatomical structures is often the first step of many medical image analysis workflows. While convolutional neural networks achieve high performance, these do not incorporate anatomical shape information. We introduce a novel segmentation algorithm that uses Deep Conditional Shape models (DCSMs) as a core component. Using deep implicit shape representations, the algorithm learns a modality-agnostic shape model that can generate the signed distance functions for any anatomy of interest. To fit the generated shape to the image, the shape model is conditioned on anatomic landmarks that can be automatically detected or provided by the user. Finally, we add a modality-dependent, lightweight refinement network to capture any fine details not represented by the implicit function. The proposed DCSM framework is evaluated on the problem of cardiac left ventricle (LV) segmentation from multiple 3D modalities (contrast-enhanced CT, non-contrasted CT, 3D echocardiography-3DE). We demonstrate that the automatic DCSM outperforms the baseline for non-contrasted CT without the local refinement, and with the refinement for contrasted CT and 3DE, especially with significant improvement in the Hausdorff distance. The semi-automatic DCSM with user-input landmarks, while only trained on contrasted CT, achieves greater than 92% Dice for all modalities. Both automatic DCSM with refinement and semi-automatic DCSM achieve equivalent or better performance compared to inter-user variability for these modalities.