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

TL;DR

EMGauss introduces a novel Gaussian splatting framework for continuous 3D reconstruction from 2D slices in volume electron microscopy, overcoming anisotropy limitations and enabling high-fidelity, isotropic 3D imaging without extensive pretraining.

Contribution

It reframes slice-to-3D reconstruction as a dynamic scene rendering problem using Gaussian splatting, with a bootstrapping mechanism for data-sparse regimes, offering a generalizable solution beyond vEM.

Findings

Significantly improves interpolation quality over diffusion and GAN methods

Enables continuous slice synthesis without large-scale pretraining

Potentially applicable across various imaging domains

Abstract

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.