The Four Color Theorem for Cell Instance Segmentation

Ye Zhang, Yu Zhou, Yifeng Wang, Jun Xiao, Ziyue Wang, Yongbing Zhang, Jianxu Chen

Abstract: Cell instance segmentation is critical to analyzing biomedical images, yet accurately distinguishing tightly touching cells remains a persistent challenge. Existing instance segmentation frameworks, including detection-based, contour-based, and distance mapping-based approaches, have made significant progress, but balancing model performance with computational efficiency remains an open problem. In this paper, we propose a novel cell instance segmentation method inspired by the four-color theorem. By conceptualizing cells as countries and tissues as oceans, we introduce a four-color encoding scheme that ensures adjacent instances receive distinct labels. This reformulation transforms instance segmentation into a constrained semantic segmentation problem with only four predicted classes, substantially simplifying the instance differentiation process. To solve the training instability caused by the non-uniqueness of four-color encoding, we design an asymptotic training strategy and encoding transformation method. Extensive experiments on various modes demonstrate our approach achieves state-of-the-art performance. The code is available at https://github.com/zhangye-zoe/FCIS.

Lay Summary:

Imagine trying to pick out every single grape in a tightly packed bunch, especially when they're squished together. That's a bit like what scientists face when trying to identify individual cells in biomedical images. It's incredibly important for understanding diseases, but current computer programs struggle to tell apart cells that are touching or overlapping, and they can be slow.

We came up with a new way to solve this problem, inspired by a map-making rule: you only need four colors to color any map so that no two bordering countries have the same color. We thought of cells as tiny countries and the surrounding tissue as the ocean.

Our method colors each cell with one of four colors. This helps the computer easily distinguish between adjacent cells. This might sound simple, but it turns the complex task of finding individual cells into a simpler one of just identifying four different patterns.

To make sure this coloring system works reliably, we developed special training techniques. Our experiments show that this new approach is very effective, achieving top performance in identifying individual cells in various types of images. We've also made our code publicly available so other researchers can use and build upon our work.

Application-Driven Machine Learning: This submission is on Application-Driven Machine Learning.

Link To Code: https://github.com/zhangye-zoe/FCIS

Primary Area: Applications->Computer Vision

Keywords: Cell instance segmentation, Four color theorem

Submission Number: 2155