Efficient Neuron Segmentation in Electron Microscopy by Affinity-Guided Queries

Accurate segmentation of neurons in electron microscopy (EM) images plays a crucial role in understanding the intricate wiring patterns of the brain. Existing automatic neuron segmentation methods rely on traditional clustering algorithms, where affinities are predicted first, and then watershed and post-processing algorithms are applied to yield segmentation results. Due to the nature of watershed algorithm, this paradigm has deficiency in both prediction quality and speed. Inspired by recent advances in natural image segmentation, we propose to use query-based methods to address the problem because they do not necessitate watershed algorithms. However, we find that directly applying existing query-based methods faces great challenges due to the large memory requirement of the 3D data and considerably different morphology of neurons. To tackle these challenges, we introduce affinity-guided queries and integrate them into a lightweight query-based framework. Specifically, we first predict affinities with a lightweight branch, which provides coarse neuron structure information. The affinities are then used to construct affinity-guided queries, facilitating segmentation with bottom-up cues. These queries, along with additional learnable queries, interact with the image features to directly predict the final segmentation results. Experiments on benchmark datasets demonstrated that our method achieved better results over state-of-the-art methods with a 2$\sim$3$\times$ speedup in inference. Code is available at https://github.com/chenhang98/AGQ.