Spatial-SAM: Spatially Consistent 3D Electron Microscopy Segmentation with SDF Memory and Semi-Supervised Learning

Segment Anything Model (SAM)-based approaches have shown strong potential for biomedical image segmentation. However, these methods often struggle to preserve spatial consistency in 3D electron microscopy (3D-EM) data and still require extensive manual annotation. We propose Spatial-SAM, a spatially consistent and annotation-efficient framework for high-precision 3D-EM segmentation. It introduces a 3D Signed Distance Field (SDF) memory mechanism that replaces SAM2's memory with SDF representations precomputed by a 3D U-Net, providing richer geometric information and improving spatial consistency. It also combines SAM2's few-shot capability with a dual-track pseudo-label iterative optimization strategy to learn largescale 3D-EM segmentation from minimal annotations. Experiments show Spatial-SAM significantly outperforms existing semi-supervised methods and performs comparably to state-of-the-art fully supervised approaches on multiple 3D-EM benchmarks, reducing annotation costs while preserving spatial consistency. Code is available at https: //github.com/Giluir/Spatial-SAM .