# Characterizing Renal Structures with 3D Block Aggregate Transformers

arXiv: https://arxiv.org/abs/2203.02430 · HTML: https://mlsanity.com/paper/2203.02430/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 23 of its 35 references that are in the map.
- First posted on arXiv 4 Mar 2022.

## Builds on (most cited first, 23 of 23)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Longformer: The Long-Document Transformer](https://mlsanity.com/paper/2004.05150/) (2020)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [Transformer in Transformer](https://mlsanity.com/paper/2103.00112/) (2021)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [Medical Transformer: Gated Axial-Attention for Medical Image Segmentation](https://mlsanity.com/paper/2102.10662/) (2021)
- [On the Relationship between Self-Attention and Convolutional Layers](https://mlsanity.com/paper/1911.03584/) (2019)
- [TransBTS: Multimodal Brain Tumor Segmentation Using Transformer](https://mlsanity.com/paper/2103.04430/) (2021)
- [TransFuse: Fusing Transformers and CNNs for Medical Image Segmentation](https://mlsanity.com/paper/2102.08005/) (2021)
- [CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.03024/) (2021)
- [The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 Challenge](https://mlsanity.com/paper/1912.01054/) (2019)
- [Nested Hierarchical Transformer: Towards Accurate, Data-Efficient and Interpretable Visual Understanding](https://mlsanity.com/paper/2105.12723/) (2021)
- [TransClaw U-Net: Claw U-Net with Transformers for Medical Image Segmentation](https://mlsanity.com/paper/2107.05188/) (2021)
- [A 3D Coarse-to-Fine Framework for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1712.00201/) (2017)
- [BiTr-Unet: a CNN-Transformer Combined Network for MRI Brain Tumor Segmentation](https://mlsanity.com/paper/2109.12271/) (2021)
- [A multi-scale pyramid of 3D fully convolutional networks for abdominal multi-organ segmentation](https://mlsanity.com/paper/1806.02237/) (2018)

## Built on by (most cited first, 2 of 2)

- [Transforming medical imaging with Transformers? A comparative review of key properties, current progresses, and future perspectives](https://mlsanity.com/paper/2206.01136/) (2022)
- [Comparison of different segmentation algorithms on brain volume and fractal dimension in infant brain MRIs](https://mlsanity.com/paper/2512.12222/) (2025)

## Abstract (arXiv)

Efficiently quantifying renal structures can provide distinct spatial context and facilitate biomarker discovery for kidney morphology. However, the development and evaluation of the transformer model to segment the renal cortex, medulla, and collecting system remains challenging due to data inefficiency. Inspired by the hierarchical structures in vision transformer, we propose a novel method using a 3D block aggregation transformer for segmenting kidney components on contrast-enhanced CT scans. We construct the first cohort of renal substructures segmentation dataset with 116 subjects under institutional review board (IRB) approval. Our method yields the state-of-the-art performance (Dice of 0.8467) against the baseline approach of 0.8308 with the data-efficient design. The Pearson R achieves 0.9891 between the proposed method and manual standards and indicates the strong correlation and reproducibility for volumetric analysis. We extend the proposed method to the public KiTS dataset, the method leads to improved accuracy compared to transformer-based approaches. We show that the 3D block aggregation transformer can achieve local communication between sequence representations without modifying self-attention, and it can serve as an accurate and efficient quantification tool for characterizing renal structures.