Helen Y. Yang

Junsik Kim, Zhiyi Shi, Davin Jeong et al.

In clinical In-Vitro Fertilization (IVF), identifying the most viable embryo for transfer is important to increasing the likelihood of a successful pregnancy. Traditionally, this process involves embryologists manually assessing embryos' static morphological features at specific intervals using light microscopy. This manual evaluation is not only time-intensive and costly, due to the need for expert analysis, but also inherently subjective, leading to variability in the selection process. To address these challenges, we develop a multimodal model that leverages both time-lapse video data and Electronic Health Records (EHRs) to predict embryo viability. One of the primary challenges of our research is to effectively combine time-lapse video and EHR data, owing to their inherent differences in modality. We comprehensively analyze our multimodal model with various modality inputs and integration approaches. Our approach will enable fast and automated embryo viability predictions in scale for clinical IVF.

Won-Dong Jang, Donglai Wei, Xingxuan Zhang et al.

Blastomere instance segmentation is important for analyzing embryos' abnormality. To measure the accurate shapes and sizes of blastomeres, their amodal segmentation is necessary. Amodal instance segmentation aims to recover the complete silhouette of an object even when the object is not fully visible. For each detected object, previous methods directly regress the target mask from input features. However, images of an object under different amounts of occlusion should have the same amodal mask output, which makes it harder to train the regression model. To alleviate the problem, we propose to classify input features into intermediate shape codes and recover complete object shapes from them. First, we pre-train the Vector Quantized Variational Autoencoder (VQ-VAE) model to learn these discrete shape codes from ground truth amodal masks. Then, we incorporate the VQ-VAE model into the amodal instance segmentation pipeline with an additional refinement module. We also detect an occlusion map to integrate occlusion information with a backbone feature. As such, our network faithfully detects bounding boxes of amodal objects. On an internal embryo cell image benchmark, the proposed method outperforms previous state-of-the-art methods. To show generalizability, we show segmentation results on the public KINS natural image benchmark. To examine the learned shape codes and model design choices, we perform ablation studies on a synthetic dataset of simple overlaid shapes. Our method would enable accurate measurement of blastomeres in in vitro fertilization (IVF) clinics, which potentially can increase IVF success rate.

Brian D. Leahy, Won-Dong Jang, Helen Y. Yang et al.

A major challenge in clinical In-Vitro Fertilization (IVF) is selecting the highest quality embryo to transfer to the patient in the hopes of achieving a pregnancy. Time-lapse microscopy provides clinicians with a wealth of information for selecting embryos. However, the resulting movies of embryos are currently analyzed manually, which is time consuming and subjective. Here, we automate feature extraction of time-lapse microscopy of human embryos with a machine-learning pipeline of five convolutional neural networks (CNNs). Our pipeline consists of (1) semantic segmentation of the regions of the embryo, (2) regression predictions of fragment severity, (3) classification of the developmental stage, and object instance segmentation of (4) cells and (5) pronuclei. Our approach greatly speeds up the measurement of quantitative, biologically relevant features that may aid in embryo selection.