# IAUNet: Instance-Aware U-Net

arXiv: https://arxiv.org/abs/2508.01928 · HTML: https://mlsanity.com/paper/2508.01928/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 25 of its 51 references that are in the map.
- First posted on arXiv 3 Aug 2025.

## Builds on (most cited first, 25 of 25)

- [Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks](https://mlsanity.com/paper/1506.01497/) (2015)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [Mask R-CNN](https://mlsanity.com/paper/1703.06870/) (2017)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [Delving Deep into Rectifiers: Surpassing Human-Level Performance on ImageNet Classification](https://mlsanity.com/paper/1502.01852/) (2015)
- [Deformable DETR: Deformable Transformers for End-to-End Object Detection](https://mlsanity.com/paper/2010.04159/) (2020)
- [Masked-attention Mask Transformer for Universal Image Segmentation](https://mlsanity.com/paper/2112.01527/) (2021)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [Rich feature hierarchies for accurate object detection and semantic segmentation](https://mlsanity.com/paper/1311.2524/) (2013)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [Per-Pixel Classification is Not All You Need for Semantic Segmentation](https://mlsanity.com/paper/2107.06278/) (2021)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Simple Copy-Paste is a Strong Data Augmentation Method for Instance Segmentation](https://mlsanity.com/paper/2012.07177/) (2020)
- [Cascade R-CNN: High Quality Object Detection and Instance Segmentation](https://mlsanity.com/paper/1906.09756/) (2019)
- [YOLOv9: Learning What You Want to Learn Using Programmable Gradient Information](https://mlsanity.com/paper/2402.13616/) (2024)
- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [Mask DINO: Towards A Unified Transformer-based Framework for Object Detection and Segmentation](https://mlsanity.com/paper/2206.02777/) (2022)
- [An Intriguing Failing of Convolutional Neural Networks and the CoordConv Solution](https://mlsanity.com/paper/1807.03247/) (2018)
- [End-to-end people detection in crowded scenes](https://mlsanity.com/paper/1506.04878/) (2015)
- [Sparse Instance Activation for Real-Time Instance Segmentation](https://mlsanity.com/paper/2203.12827/) (2022)
- [Micro-Net: A unified model for segmentation of various objects in microscopy images](https://mlsanity.com/paper/1804.08145/) (2018)
- [InstanceCut: from Edges to Instances with MultiCut](https://mlsanity.com/paper/1611.08272/) (2016)
- [Attention-Based Transformers for Instance Segmentation of Cells in Microstructures](https://mlsanity.com/paper/2011.09763/) (2020)
- [FastInst: A Simple Query-Based Model for Real-Time Instance Segmentation](https://mlsanity.com/paper/2303.08594/) (2023)
- [Oriented Boxes for Accurate Instance Segmentation](https://mlsanity.com/paper/1911.07732/) (2019)

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

- [Single Tensor Cell Segmentation using Scalar Field Representations](https://mlsanity.com/paper/2511.13947/) (2025)

## Abstract (arXiv)

Instance segmentation is critical in biomedical imaging to accurately distinguish individual objects like cells, which often overlap and vary in size. Recent query-based methods, where object queries guide segmentation, have shown strong performance. While U-Net has been a go-to architecture in medical image segmentation, its potential in query-based approaches remains largely unexplored. In this work, we present IAUNet, a novel query-based U-Net architecture. The core design features a full U-Net architecture, enhanced by a novel lightweight convolutional Pixel decoder, making the model more efficient and reducing the number of parameters. Additionally, we propose a Transformer decoder that refines object-specific features across multiple scales. Finally, we introduce the 2025 Revvity Full Cell Segmentation Dataset, a unique resource with detailed annotations of overlapping cell cytoplasm in brightfield images, setting a new benchmark for biomedical instance segmentation. Experiments on multiple public datasets and our own show that IAUNet outperforms most state-of-the-art fully convolutional, transformer-based, and query-based models and cell segmentation-specific models, setting a strong baseline for cell instance segmentation tasks. Code is available at https://github.com/SlavkoPrytula/IAUNet