# 3D Cell Oversegmentation Correction via Geo-Wasserstein Divergence

arXiv: https://arxiv.org/abs/2502.01890 · HTML: https://mlsanity.com/paper/2502.01890/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 15 of its 42 references that are in the map.
- First posted on arXiv 3 Feb 2025.

## Builds on (most cited first, 15 of 15)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://mlsanity.com/paper/2003.07311/) (2020)
- [Topology-Preserving Deep Image Segmentation](https://mlsanity.com/paper/1906.05404/) (2019)
- [Cell Detection with Star-convex Polygons](https://mlsanity.com/paper/1806.03535/) (2018)
- [DCAN: Deep Contour-Aware Networks for Accurate Gland Segmentation](https://mlsanity.com/paper/1604.02677/) (2016)
- [Topology-Aware Segmentation Using Discrete Morse Theory](https://mlsanity.com/paper/2103.09992/) (2021)
- [Micro-Net: A unified model for segmentation of various objects in microscopy images](https://mlsanity.com/paper/1804.08145/) (2018)
- [Topologically faithful image segmentation via induced matching of persistence barcodes](https://mlsanity.com/paper/2211.15272/) (2022)
- [Star-convex Polyhedra for 3D Object Detection and Segmentation in Microscopy](https://mlsanity.com/paper/1908.03636/) (2019)
- [Combining Fully Convolutional and Recurrent Neural Networks for 3D Biomedical Image Segmentation](https://mlsanity.com/paper/1609.01006/) (2016)
- [Topograph: An efficient Graph-Based Framework for Strictly Topology Preserving Image Segmentation](https://mlsanity.com/paper/2411.03228/) (2024)
- [Omni-Seg: A Scale-aware Dynamic Network for Renal Pathological Image Segmentation](https://mlsanity.com/paper/2206.13632/) (2022)
- [Monge, Bregman and Occam: Interpretable Optimal Transport in High-Dimensions with Feature-Sparse Maps](https://mlsanity.com/paper/2302.04065/) (2023)
- [Robust 3D Cell Segmentation: Extending the View of Cellpose](https://mlsanity.com/paper/2105.00794/) (2021)

## Abstract (arXiv)

3D cell segmentation methods are often hindered by 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 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, Geo-Wasserstein divergence, to quantify changes in 2D geometries. This captures the evolving trends of cell mask shape in a geometry-aware manner. We validate our method through extensive experiments on in-domain plant datasets, including both synthesized and real oversegmented cases, as well as on out-of-domain animal datasets to demonstrate transfer learning performance. An ablation study further highlights the contribution of the Geo-Wasserstein divergence. A clear pipeline is provided for end-users to build pre-trained models to any labeled dataset.