NuGraph: Graph-Based Reasoning over 3D Primitives for Nucleus Segmentation Correction

Abstract

Correcting segmentation errors in large-scale 3D nuclei reconstructions requires reasoning about which fragments belong to the same nucleus across densely packed regions. Existing correction methods rely on local pairwise fragment matching, which cannot resolve the global topology of nuclear clusters and fails to recover missing morphology. We propose NO_SCPLOWUC_SCPLOWGO_SCPLOWRAPHC_SCPLOW, a graph-based reasoning framework that operates over atomic 3D primitives obtained by decomposing erroneous masks. NO_SCPLOWUC_SCPLOWGO_SCPLOWRAPHC_SCPLOW encodes primitive geometry via a 3D point-cloud backbone and performs global relational reasoning through graph attention, capturing inter-primitive dependencies across entire clusters rather than isolated pairs. A primitive-proposal contrastive loss aligns local primitive features with nucleuslevel semantics, improving grouping accuracy in dense regions. The resulting proposals are then refined by a shaperefinement network that predicts signed distance fields to restore smooth morphology. To train without manual error annotations, we develop a self-supervised data engine that synthesizes realistic segmentation errors from clean nuclei labels. To benchmark correction at brain scale, we curate NucEMFix, the first brain-wide EM benchmark of nuclei error cases across FAFB and MICrONS (8,000+ annotated error nuclei). NO_SCPLOWUC_SCPLOWGO_SCPLOWRAPHC_SCPLOW attains 87.99% F1 on NucEMFix-F (FAFB) and 86.20% on NucEMFix-M (MICrONS), outperforming both re-segmentation baselines (e.g., +8.6% over nnU-Net) and pairwise correction methods, while reducing curation effort by over 100x relative to manual proofreading. Code and data are available at https://mingzhiwang618.github.io/NucEMFix.