Ensemble of Deep Learning Cascades for Segmentation of Blood Vessels in Confocal Microscopy Images

Detection, segmentation, and quantification of microvascular structures are the main steps towards studying microvascular remodeling. Combined with appropriate staining, confocal microscopy imaging enables exploration of the full 3D anatomical characteristics of microvascular systems. Segmentation of confocal microscopy images is a challenging task due to complexity of anatomical structures, staining and imaging issues, and lack of annotated training data. In this paper, we propose a deep learning system for robust segmentation of cranial vasculature of mice in confocal microscopy images. The proposed system is an ensemble of two deep-learning cascades consisting of two coarse-to-fine subnetworks with skip connections in between. One cascade aims to improve sensitivity, while the other aims to improve precision of the segmentation results. Our experiments on mice cranial vasculature showed promising results achieving segmentation accuracy of 92.02% and dice score of 81.45% despite being trained on very limited confocal microscopy data.