Data-driven Morphological Feature Perception of Single Neuron with Graph Neural Network.

Abstract

Clarifying the morphological characteristics of neurons can promote the understanding of brain function. However, traditional morphometrics fail to capture the modeling of each point in reconstructed neurons, leading to limited ability to distinguish massive nerve fibers and restricted application scenarios. To address these challenges, we propose MorphoGNN, a single neuron morphological embedding based on a graph neural network in this study. MorphoGNN learns the point-level structure information of reconstructed nerve fibers by considering their nearest neighbors on each hidden layer. This enables MorphoGNN to capture the lower-dimensional representation of a single neuron through an end-to-end model. In order to meet the requirements of various tasks, both supervised and self-supervised training strategies are designed to learn the characteristics that fit artificial semantics or the morphological patterns of neurons, respectively. We quantitatively compare our embeddings with other features in neuron classification and retrieval tasks and demonstrate cutting-edge performance. Additionally, we introduce our embeddings to the task of reconstruction quality classification and neuron clustering, where they can help detect reconstruction errors and obtain similar subtyping results to existing work. Furthermore, our method can be handily combined with other modal features, such as microscopic image features and traditional morphometrics. Ablation and robustness tests are also conducted to analyze the impact of several network components and low-quality reconstructed neurons on the performance of our method. The code is available at https://github.com/fun0515/MorphoGNN.