Adaptive Template Transformer for Mitochondria Segmentation in Electron Microscopy Images

Abstract

Mitochondria, as tiny structures within the cell, are of significant importance in studying cell functions for biological and clinical analysis. And exploring how to automatically segment mitochondria in electron microscopy (EM) images has attracted increasing attention. However, most of existing methods struggle to adapt to different scales and appearances of the input due to the inherent limitations of the traditional CNN architecture. To mitigate these limitations, we propose a novel adaptive template transformer (ATFormer) for mitochondria segmentation. The proposed ATFormer model enjoys several merits. First, the designed structural template learning module can acquire appearance-adaptive templates of background, foreground and contour to sense the characteristics of different shapes of mitochondria. And we further adopt an optimal transport algorithm to enlarge the discrepancy among diverse templates to activate corresponding regions fully. Second, we introduce a hierarchical attention learning mechanism to absorb multi-level information for templates to be adaptive scale-aware classifiers for dense prediction. Extensive experimental results on three challenging benchmarks including MitoEM, Lucchi and NucMM-Z datasets demonstrate that our ATFormer performs favorably against state-of-the-art mitochondria segmentation methods.