ShapeMamba-EM: Fine-Tuning Foundation Model with Local Shape Descriptors and Mamba Blocks for 3D EM Image Segmentation

Abstract: Electron microscopy (EM) imaging offers unparalleled resolution for analyzing neural tissues, crucial for uncovering the intricacies of synaptic connections and neural processes fundamental to understanding behavioral mechanisms. Recently, the foundation models have demonstrated impressive performance across numerous natural and medical image segmentation tasks. However, applying these foundation models to EM segmentation faces significant challenges due to domain disparities. This paper presents ShapeMamba-EM, a specialized fine-tuning method for 3D EM segmentation, which employs adapters for long-range dependency modeling and an encoder for local shape description within the original foundation model. This approach effectively addresses the unique volumetric and morphological complexities of EM data. Tested over a wide range of EM images, covering five segmentation tasks and 10 datasets, ShapeMamba-EM outperforms existing methods, establishing a new standard in EM image segmentation and enhancing the understanding of neural tissue architecture.