FIB-SEMBench: A Benchmark for Isotropic Super-Resolution of FIB-SEM Volumes

Volumetric electron microscopy, particularly focused ion beam scanning electron microscopy (FIB-SEM), enables three-dimensional visualization of cellular ultrastructure, but acquiring high-resolution isotropic volumes is constrained by high cost and low throughput. 3D super-resolution (SR) offers a way to recover details from low-resolution volumes, while existing SR evaluations rely mainly on image-fidelity metrics. Whether higher image-level fidelity reflects faithful 3D structure or accurate mitochondrial volume estimates remains unclear. To examine this issue, we present FIB-SEMBench, a standardized benchmark for $2\times$ isotropic SR ($8\to 4\text{nm}$). The benchmark covers four biologically diverse datasets spanning mouse and Drosophila tissues, with a physics-inspired degradation pipeline and spatially separated data partitioning. We benchmark four 3D SR approaches in terms of image-level fidelity, 3D structural preservation, mitochondrial volume accuracy, and computational efficiency. Our evaluation reveals that higher image-level fidelity does not necessarily correspond to better 3D structure preservation or more accurate mitochondrial volume estimates.