TransNuSeg: A Lightweight Multi-Task Transformer for Nuclei Segmentation

TL;DR

TransNuSeg introduces a lightweight, multi-task Transformer framework for nuclei segmentation that outperforms existing CNN-based methods by leveraging shared attention and self-distillation, reducing complexity while maintaining high accuracy.

Contribution

It is the first pure Transformer approach for nuclei segmentation, employing multi-task learning, attention sharing, and a token MLP bottleneck to improve efficiency and accuracy.

Findings

Outperforms state-of-the-art methods by 2-3% Dice score.

Uses 30% fewer parameters than comparable models.

Effective in different modality datasets.

Abstract

Nuclei appear small in size, yet, in real clinical practice, the global spatial information and correlation of the color or brightness contrast between nuclei and background, have been considered a crucial component for accurate nuclei segmentation. However, the field of automatic nuclei segmentation is dominated by Convolutional Neural Networks (CNNs), meanwhile, the potential of the recently prevalent Transformers has not been fully explored, which is powerful in capturing local-global correlations. To this end, we make the first attempt at a pure Transformer framework for nuclei segmentation, called TransNuSeg. Different from prior work, we decouple the challenging nuclei segmentation task into an intrinsic multi-task learning task, where a tri-decoder structure is employed for nuclei instance, nuclei edge, and clustered edge segmentation respectively. To eliminate the divergent predictions from different branches in previous work, a novel self distillation loss is introduced to explicitly impose consistency regulation between branches. Moreover, to formulate the high correlation between branches and also reduce the number of parameters, an efficient attention sharing scheme is proposed by partially sharing the self-attention heads amongst the tri-decoders. Finally, a token MLP bottleneck replaces the over-parameterized Transformer bottleneck for a further reduction in model complexity. Experiments on two datasets of different modalities, including MoNuSeg have shown that our methods can outperform state-of-the-art counterparts such as CA2.5-Net by 2-3% Dice with 30% fewer parameters. In conclusion, TransNuSeg confirms the strength of Transformer in the context of nuclei segmentation, which thus can serve as an efficient solution for real clinical practice. Code is available at https://github.com/zhenqi-he/transnuseg.