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Geometric Framework for Cell Oversegmentation

3D cell segmentation methods are often hindered by \emph{oversegmentation}, where a single cell is incorrectly split into multiple fragments. This degrades the final segmentation quality and is notoriously difficult to resolve, as oversegmentation errors often resemble \emph{natural gaps} between adjacent cells. Our work makes two key contributions. First, for 3D cell segmentation, we are the first work to formulate oversegmentation as a concrete problem and propose a geometric framework to identify and correct these errors. Our approach builds a pre-trained classifier using both 2D geometric and 3D topological features extracted from flawed 3D segmentation results. Second, we introduce a novel metric, \emph{Geo-Wasserstein} divergence, to quantify changes in 2D geometries. This captures the evolving trends in cell mask shape changes in a geometry-aware manner. We validate our method through extensive experiments on in-domain plant datasets, including both synthesized and real cases, as well as on out-of-domain animal datasets to demonstrate transfer learning performance. An ablation study further highlights the contribution of the \emph{Geo-Wasserstein} divergence. A clear pipeline is provided for end-users to build pre-trained models to any labeled dataset.

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