Régine P.M. Steegers‐Theunissen

W. A. P. Bastiaansen, M. Rousian, R. P. M. Steegers-Theunissen et al.

Segmentation and spatial alignment of ultrasound (US) imaging data acquired in the in first trimester are crucial for monitoring human embryonic growth and development throughout this crucial period of life. Current approaches are either manual or semi-automatic and are therefore very time-consuming and prone to errors. To automate these tasks, we propose a multi-atlas framework for automatic segmentation and spatial alignment of the embryo using deep learning with minimal supervision. Our framework learns to register the embryo to an atlas, which consists of the US images acquired at a range of gestational age (GA), segmented and spatially aligned to a predefined standard orientation. From this, we can derive the segmentation of the embryo and put the embryo in standard orientation. US images acquired at 8+0 till 12+6 weeks GA were used and eight subjects were selected as atlas. We evaluated different fusion strategies to incorporate multiple atlases: 1) training the framework using atlas images from a single subject, 2) training the framework with data of all available atlases and 3) ensembling of the frameworks trained per subject. To evaluate the performance, we calculated the Dice score over the test set. We found that training the framework using all available atlases outperformed ensembling and gave similar results compared to the best of all frameworks trained on a single subject. Furthermore, we found that selecting images from the four atlases closest in GA out of all available atlases, regardless of the individual quality, gave the best results with a median Dice score of 0.72. We conclude that our framework can accurately segment and spatially align the embryo in first trimester 3D US images and is robust for the variation in quality that existed in the available atlases.

Wietske A. P. Bastiaansen, Melek Rousian, Régine P. M. Steegers-Theunissen et al.

We propose an unsupervised deep learning method for atlas based registration to achieve segmentation and spatial alignment of the embryonic brain in a single framework. Our approach consists of two sequential networks with a specifically designed loss function to address the challenges in 3D first trimester ultrasound. The first part learns the affine transformation and the second part learns the voxelwise nonrigid deformation between the target image and the atlas. We trained this network end-to-end and validated it against a ground truth on synthetic datasets designed to resemble the challenges present in 3D first trimester ultrasound. The method was tested on a dataset of human embryonic ultrasound volumes acquired at 9 weeks gestational age, which showed alignment of the brain in some cases and gave insight in open challenges for the proposed method. We conclude that our method is a promising approach towards fully automated spatial alignment and segmentation of embryonic brains in 3D ultrasound.