# A General Pipeline for Glomerulus Whole-Slide Image Segmentation

arXiv: https://arxiv.org/abs/2411.04782 · HTML: https://mlsanity.com/paper/2411.04782/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 11 of its 22 references that are in the map.
- First posted on arXiv 7 Nov 2024.

## Builds on (most cited first, 11 of 11)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [A ConvNet for the 2020s](https://mlsanity.com/paper/2201.03545/) (2022)
- [Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation](https://mlsanity.com/paper/1802.02611/) (2018)
- [SegFormer: Simple and Efficient Design for Semantic Segmentation with Transformers](https://mlsanity.com/paper/2105.15203/) (2021)
- [Masked-attention Mask Transformer for Universal Image Segmentation](https://mlsanity.com/paper/2112.01527/) (2021)
- [Unified Perceptual Parsing for Scene Understanding](https://mlsanity.com/paper/1807.10221/) (2018)
- [Quantifying the effects of data augmentation and stain color normalization in convolutional neural networks for computational pathology](https://mlsanity.com/paper/1902.06543/) (2019)
- [HoloHisto: End-to-end Gigapixel WSI Segmentation with 4K Resolution Sequential Tokenization](https://mlsanity.com/paper/2407.03307/) (2024)
- [New Descriptor for Glomerulus Detection in Kidney Microscopy Image](https://mlsanity.com/paper/1506.05920/) (2015)

## Abstract (arXiv)

Whole-slide images (WSI) glomerulus segmentation is essential for accurately diagnosing kidney diseases. In this work, we propose a general and practical pipeline for glomerulus segmentation that effectively enhances both patch-level and WSI-level segmentation tasks. Our approach leverages stitching on overlapping patches, increasing the detection coverage, especially when glomeruli are located near patch image borders. In addition, we conduct comprehensive evaluations from different segmentation models across two large and diverse datasets with over 30K glomerulus annotations. Experimental results demonstrate that models using our pipeline outperform the previous state-of-the-art method, achieving superior results across both datasets and setting a new benchmark for glomerulus segmentation in WSIs. The code and pre-trained models are available at https://github.com/huuquan1994/wsi_glomerulus_seg.