TreeMoCo: Contrastive Neuron Morphology Representation Learning

Part of Advances in Neural Information Processing Systems 35 (NeurIPS 2022) Main Conference Track

Bibtex Paper Supplemental


Hanbo Chen, Jiawei Yang, Daniel Iascone, Lijuan Liu, Lei He, Hanchuan Peng, Jianhua Yao


Morphology of neuron trees is a key indicator to delineate neuronal cell-types, analyze brain development process, and evaluate pathological changes in neurological diseases. Traditional analysis mostly relies on heuristic features and visual inspections. A quantitative, informative, and comprehensive representation of neuron morphology is largely absent but desired. To fill this gap, in this work, we adopt a Tree-LSTM network to encode neuron morphology and introduce a self-supervised learning framework named TreeMoCo to learn features without the need for labels. We test TreeMoCo on 2403 high-quality 3D neuron reconstructions of mouse brains from three different public resources. Our results show that TreeMoCo is effective in both classifying major brain cell-types and identifying sub-types. To our best knowledge, TreeMoCo is the very first to explore learning the representation of neuron tree morphology with contrastive learning. It has a great potential to shed new light on quantitative neuron morphology analysis. Code is available at