Thumbnails of dendrites are randomly colored.

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.

The formulas of these two metrics are detailed in Sec. Figure A1 (a), by only re-ordering of edge vectors, a branch's shape can be significantly changed Such measurement is taken in a bag-of-word (BOW) fashion. The context and spatial relationship between arbors are ignored under this measurement. Branch A and B are composed of the same set of edge vectors. Each neuron is viewed from three different angles. Three public datasets are used in this study.

Traditional analysis mostly relies on heuristic features and visual inspections.

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.