# Going Beyond U-Net: Assessing Vision Transformers for Semantic Segmentation in Microscopy Image Analysis

arXiv: https://arxiv.org/abs/2409.16940 · HTML: https://mlsanity.com/paper/2409.16940/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 17 of its 31 references that are in the map.
- First posted on arXiv 25 Sep 2024.

## Builds on (most cited first, 17 of 17)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [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)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [Feature Pyramid Networks for Object Detection](https://mlsanity.com/paper/1612.03144/) (2016)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [Rethinking Semantic Segmentation from a Sequence-to-Sequence Perspective with Transformers](https://mlsanity.com/paper/2012.15840/) (2020)
- [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)
- [Spatial Pyramid Pooling in Deep Convolutional Networks for Visual Recognition](https://mlsanity.com/paper/1406.4729/) (2014)
- [Generalised Dice overlap as a deep learning loss function for highly unbalanced segmentations](https://mlsanity.com/paper/1707.03237/) (2017)
- [Albumentations: fast and flexible image augmentations](https://mlsanity.com/paper/1809.06839/) (2018)
- [SUNet: Swin Transformer UNet for Image Denoising](https://mlsanity.com/paper/2202.14009/) (2022)
- [SSformer: A Lightweight Transformer for Semantic Segmentation](https://mlsanity.com/paper/2208.02034/) (2022)

## Built on by (most cited first, 1 of 1)

- [Prompt-Tuning SAM: From Generalist to Specialist with only 2048 Parameters and 16 Training Images](https://mlsanity.com/paper/2504.16739/) (2025)

## Abstract (arXiv)

Segmentation is a crucial step in microscopy image analysis. Numerous approaches have been developed over the past years, ranging from classical segmentation algorithms to advanced deep learning models. While U-Net remains one of the most popular and well-established models for biomedical segmentation tasks, recently developed transformer-based models promise to enhance the segmentation process of microscopy images. In this work, we assess the efficacy of transformers, including UNETR, the Segment Anything Model, and Swin-UPerNet, and compare them with the well-established U-Net model across various image modalities such as electron microscopy, brightfield, histopathology, and phase-contrast. Our evaluation identifies several limitations in the original Swin Transformer model, which we address through architectural modifications to optimise its performance. The results demonstrate that these modifications improve segmentation performance compared to the classical U-Net model and the unmodified Swin-UPerNet. This comparative analysis highlights the promise of transformer models for advancing biomedical image segmentation. It demonstrates that their efficiency and applicability can be improved with careful modifications, facilitating their future use in microscopy image analysis tools.