TriSAM: Tri-Plane SAM for zero-shot cortical blood vessel segmentation in VEM images

In this paper, we address a significant gap in the field of neuroimaging by introducing the largest-to-date public benchmark, BvEM, designed specifically for cortical blood vessel segmentation in Volume Electron Microscopy (VEM) images. The intricate relationship between cerebral blood vessels and neural function underscores the vital role of vascular analysis in understanding brain health. While imaging techniques at macro and mesoscales have garnered substantial attention and resources, the microscale VEM imaging, capable of revealing intricate vascular details, has lacked the necessary benchmarking infrastructure. As researchers delve deeper into the microscale intricacies of cerebral vasculature, our BvEM benchmark represents a critical step toward unraveling the mysteries of neurovascular coupling and its impact on brain function and pathology. The BvEM dataset is based on VEM image volumes from three mammal species: adult mouse, macaque, and human. We standardized the resolution, addressed imaging variations, and meticulously annotated blood vessels through semi-automatic, manual, and quality control processes, ensuring high-quality 3D segmentation. Furthermore, we developed a zero-shot cortical blood vessel segmentation method named TriSAM, which leverages the powerful segmentation model SAM for 3D segmentation. To lift SAM from 2D segmentation to 3D volume segmentation, TriSAM employs a multi-seed tracking framework, leveraging the reliability of certain image planes for tracking while using others to identify potential turning points. This approach, consisting of Tri-Plane selection, SAM-based tracking, and recursive redirection, effectively achieves long-term 3D blood vessel segmentation without model training or fine-tuning. Experimental results show that TriSAM achieved superior performances on the BvEM benchmark across three species.