# trAIce3D: A Prompt-Driven Transformer Based U-Net for Semantic Segmentation of Microglial Cells from Large-Scale 3D Microscopy Images

arXiv: https://arxiv.org/abs/2507.22635 · HTML: https://mlsanity.com/paper/2507.22635/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 26 references that are in the map.
- First posted on arXiv 30 Jul 2025.

## Builds on (most cited first, 14 of 14)

- [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)
- [FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness](https://mlsanity.com/paper/2205.14135/) (2022)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [PointRend: Image Segmentation as Rendering](https://mlsanity.com/paper/1912.08193/) (2019)
- [clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://mlsanity.com/paper/2003.07311/) (2020)
- [TransBTS: Multimodal Brain Tumor Segmentation Using Transformer](https://mlsanity.com/paper/2103.04430/) (2021)
- [TorchIO: A Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning](https://mlsanity.com/paper/2003.04696/) (2020)
- [Robust 3D Cell Segmentation: Extending the View of Cellpose](https://mlsanity.com/paper/2105.00794/) (2021)

## Abstract (arXiv)

The shape of a cell contains essential information about its function within the biological system. Segmenting these structures from large-scale 3D microscopy images is challenging, limiting clinical insights especially for microglia, immune-associated cells involved in neurodegenerative diseases. Existing segmentation methods mainly focus on cell bodies, struggle with overlapping structures, perform poorly on noisy images, require hyperparameter tuning for each new dataset, or rely on tedious semi-automated approaches. We introduce trAIce3D, a deep-learning architecture designed for precise microglia segmentation, capturing both somas and branches. It employs a two-stage approach: first, a 3D U-Net with vision transformers in the encoder detects somas using a sliding-window technique to cover the entire image. Then, the same architecture, enhanced with cross-attention blocks in skip connections, refines each soma and its branches by using soma coordinates as a prompt and a 3D window around the target cell as input. Training occurs in two phases: self-supervised Soma Segmentation, followed by prompt-based Branch Segmentation, leveraging pre-trained weights from the first phase. Trained and evaluated on a dataset of 41,230 microglial cells, trAIce3D significantly improves segmentation accuracy and generalization, enabling scalable analysis of complex cellular morphologies. While optimized for microglia, its architecture can extend to other intricate cell types, such as neurons and astrocytes, broadening its impact on neurobiological research.