J-Invariant Volume Shuffle for Self-Supervised Cryo-Electron Tomogram Denoising on Single Noisy Volume

Xiwei Liu, Mohamad Kassab, Min Xu, Qirong Ho; Proceedings of the Winter Conference on Applications of Computer Vision (WACV), 2025, pp. 568-577

Cryo-Electron Tomography (Cryo-ET) enables detailed 3D visualization of cellular structures in near-native states but suffers from low signal-to-noise ratio due to imaging constraints. Traditional denoising methods and supervised learning approaches often struggle with complex noise patterns and the lack of paired datasets. Self-supervised methods which utilize noisy input itself as a target have been studied; however existing Cryo-ET self-supervised denoising methods face significant challenges due to losing information during training and the learned incomplete noise patterns. In this paper we propose a novel self-supervised learning model that denoises Cryo-ET volumetric images using a single noisy volume. Our method features a U-shape J-invariant blind spot network with sparse centrally masked convolutions dilated channel attention blocks and volume-unshuffle/shuffle technique. The volume-unshuffle/shuffle technique expands receptive fields and utilizes multi-scale representations significantly improving noise reduction and structural preservation. Experimental results demonstrate that our approach achieves superior performance compared to existing methods advancing Cryo-ET data processing for structural biology research.