Re-Isotropic Segmentation for Subcellular Ultrastructure in Anisotropic EM Images

Despite advances in ultrathin cutting, serial sections in electron microscopy (EM) still exhibit noticeable anisotropy, with much lower z-axis resolution compared with the other two axes. As a result, the imaged biovolume suffers from low connectivity smoothness in contextual structures, which makes the subcellular ultrastructural segmentation challenging. The recent 2.5D hybrid convolutions allow the direct learning of asymmetric semantics from anisotropic features. However, plain representations without the isotropic scale prior limit the performance of the upper bound. This paper presents a novel framework, referred to as ReIsoSeg, which aims at incorporating an isotropic scaling prior into anisotropic biovolumes. More precisely, ReIsoSeg consists of an anisotropic primary encoder, a pseudo-isotropic auxiliary module, and a weight-shared decoder. The auxiliary module implicitly deforms the anisotropic features from the primary encoder to align with the isotropic prior. The re-isotropic loss squeezes the pseudo-isotropic representations into the anisotropic space to reuse the anisotropic labels. The shared decoder ensures that the outputs of the anisotropic encoder converge towards the isotropic representations. During the inference process, the auxiliary module is excluded. Comprehensive experiments were conducted on the AC3/AC4, CREMI, and MitoEM subcellular ultrastructure datasets. The obtained results demonstrate the high performance of the proposed ReIsoSeg.