# Multi-scale Multi-site Renal Microvascular Structures Segmentation for Whole Slide Imaging in Renal Pathology

arXiv: https://arxiv.org/abs/2308.05782 · HTML: https://mlsanity.com/paper/2308.05782/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 6 of its 16 references that are in the map.
- First posted on arXiv 10 Aug 2023.

## Builds on (most cited first, 6 of 6)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Group Normalization](https://mlsanity.com/paper/1803.08494/) (2018)
- [DoDNet: Learning to segment multi-organ and tumors from multiple partially labeled datasets](https://mlsanity.com/paper/2011.10217/) (2020)
- [Fast Image Processing with Fully-Convolutional Networks](https://mlsanity.com/paper/1709.00643/) (2017)
- [Multi-Scale Coarse-to-Fine Segmentation for Screening Pancreatic Ductal Adenocarcinoma](https://mlsanity.com/paper/1807.02941/) (2018)
- [Omni-Seg: A Single Dynamic Network for Multi-label Renal Pathology Image Segmentation using Partially Labeled Data](https://mlsanity.com/paper/2112.12665/) (2021)

## Abstract (arXiv)

Segmentation of microvascular structures, such as arterioles, venules, and capillaries, from human kidney whole slide images (WSI) has become a focal point in renal pathology. Current manual segmentation techniques are time-consuming and not feasible for large-scale digital pathology images. While deep learning-based methods offer a solution for automatic segmentation, most suffer from a limitation: they are designed for and restricted to training on single-site, single-scale data. In this paper, we present Omni-Seg, a novel single dynamic network method that capitalizes on multi-site, multi-scale training data. Unique to our approach, we utilize partially labeled images, where only one tissue type is labeled per training image, to segment microvascular structures. We train a singular deep network using images from two datasets, HuBMAP and NEPTUNE, across different magnifications (40x, 20x, 10x, and 5x). Experimental results indicate that Omni-Seg outperforms in terms of both the Dice Similarity Coefficient (DSC) and Intersection over Union (IoU). Our proposed method provides renal pathologists with a powerful computational tool for the quantitative analysis of renal microvascular structures.