Analysis Pipeline to Quantify Uterine Gland Structural Variations

Technical advances in whole tissue imaging and clearing have allowed 3D reconstruction of exocrine uterine glands deep seated in the endometrium. However, there are limited gland structure analysis platforms to analyze these imaging data sets. Here we present a pipeline for segmenting and analyzing uterine gland shape. Using this segmentation methodology, we derive individual metrics to describe gland length, shape, and branching patterns. These metrics are applied to quantify gland behavior with respect to organization around the embryo and proximity of each individual unit to the uterine lumen. Using this image analysis pipeline we evaluate uterine glands at the peri-implantation time points of a mouse pregnancy. Our analysis reveals that upon embryo entry into the uterus glands show changes in length, tortuosity, and proximity to the uterine lumen while gland branch number stays the same. These shape changes aid in reorganization of the glands around the site of embryo implantation. We further apply our analysis pipeline to human and guinea pig uterine glands, extending feasibility to other mammalian species. This work serves as a resource for researchers to extract quantitative, reproducible morphological features from three-dimensional uterine gland images in order to reveal insights about functional and structural patterns.