EMGauss: Continuous Slice-to-3D Reconstruction via Dynamic Gaussian Modeling in Volume Electron Microscopy

Volume electron microscopy (vEM) enables nanoscale 3D imaging of biological structures but remains constrained by acquisition trade-offs, leading to anisotropic volumes with limited axial resolution. Existing deep learning methods seek to restore isotropy by leveraging lateral priors; yet their assumptions break down for morphologically anisotropic structures. We present EMGauss, a general framework for 3D reconstruction from planar scanned 2D slices with applications in vEM, which circumvents the inherent limitations of isotropy-based approaches. Our key innovation is to reframe slice-to-3D reconstruction as a 3D dynamic scene rendering problem based on Gaussian splatting, where the progression of axial slices is modeled as the temporal evolution of 2D Gaussian point clouds. To enhance fidelity in data-sparse regimes, we incorporate a Teacher–Student bootstrapping mechanism that uses high-confidence predictions on unobserved slices as pseudo-supervisory signals. Compared with diffusion- and GAN-based reconstruction methods, EMGauss substantially improves interpolation quality, enables continuous slice synthesis, and eliminates the need for large-scale pretraining. Beyond vEM, it potentially provides a generalizable slice-to-3D solution across diverse imaging domains.