Robust semi-automatic vessel tracing in the human retinal image by an instance segmentation neural network

The morphology and hierarchy of the vascular systems are essential for perfusion in supporting metabolism. In human retina, one of the most energy-demanding organs, retinal circulation nourishes the entire inner retina by an intricate vasculature emerging and remerging at the optic nerve head (ONH). Thus, tracing the vascular branching from ONH through the vascular tree can illustrate vascular hierarchy and allow detailed morphological quantification, and yet remains a challenging task. Here, we presented a novel approach for a robust semi-automatic vessel tracing algorithm on human fundus images by an instance segmentation neural network (InSegNN). Distinct from semantic segmentation, InSegNN separates and labels different vascular trees individually and therefore enable tracing each tree throughout its branching. We have built-in three strategies to improve robustness and accuracy with temporal learning, spatial multi-sampling, and dynamic probability map. We achieved 83% specificity, and 50% improvement in Symmetric Best Dice (SBD) compared to literature, and outperformed baseline U-net. We have demonstrated tracing individual vessel trees from fundus images, and simultaneously retain the vessel hierarchy information. InSegNN paves a way for any subsequent morphological analysis of vascular morphology in relation to retinal diseases

STEm-Seg: Spatio-temporal Embeddings for Instance Segmentation in Videos

Existing methods for instance segmentation in videos typi-cally involve multi-stage pipelines that follow the tracking-by-detectionparadigm and model a video clip as a sequence of images. Multiple net-works are used to detect objects in individual frames, and then associatethese detections over time. Hence, these methods are often non-end-to-end trainable and highly tailored to specific tasks. In this paper, we pro-pose a different approach that is well-suited to a variety of tasks involvinginstance segmentation in videos. In particular, we model a video clip asa single 3D spatio-temporal volume, and propose a novel approach thatsegments and tracks instances across space and time in a single stage. Ourproblem formulation is centered around the idea of spatio-temporal em-beddings which are trained to cluster pixels belonging to a specific objectinstance over an entire video clip. To this end, we introduce (i) novel mix-ing functions that enhance the feature representation of spatio-temporalembeddings, and (ii) a single-stage, proposal-free network that can rea-son about temporal context. Our network is trained end-to-end to learnspatio-temporal embeddings as well as parameters required to clusterthese embeddings, thus simplifying inference. Our method achieves state-of-the-art results across multiple datasets and tasks. Code and modelsare available at https://github.com/sabarim/STEm-Seg.Comment: 28 pages, 6 figure