Neural Information Processing Systems http://nips.cc/

Neural Information Processing Systems http://nips.cc/

Identifying cerebral cortex layers is crucial for comparative studies of the cytoarchitecture aiming at providing insights into the relations between brain structure and function across species. The absence of extensive annotated datasets typically limits the adoption of machine learning approaches, leading to the manual delineation of cortical layers by neuroanatomists. We introduce a self-supervised approach to detect layers in 2D Nissl-stained histological slices of the cerebral cortex. It starts with the segmentation of individual cells and the creation of an attributed cell-graph. A self-supervised graph convolutional network generates cell embeddings that encode morphological and structural traits of the cellular environment and are exploited by a community detection algorithm for the final layering. Our method, the first self-supervised of its kind with no spatial transcriptomics data involved, holds the potential to accelerate cytoarchitecture analyses, sidestepping annotation needs and advancing cross-species investigation.

Understanding the diversity of cell types and their function in the brain is one of the key challenges in neuroscience. The advent of large-scale datasets has given rise to the need of unbiased and quantitative approaches to cell type classification. We present GraphDINO, a purely data-driven approach to learning a low dimensional representation of the 3D morphology of neurons. GraphDINO is a novel graph representation learning method for spatial graphs utilizing self-supervised learning on transformer models. It smoothly interpolates between attention-based global interaction between nodes and classic graph convolutional processing. We show that this method is able to yield morphological cell type clustering that is comparable to manual feature-based classification and shows a good correspondence to expert-labeled cell types in two different species and cortical areas. Our method is applicable beyond neuroscience in settings where samples in a dataset are graphs and graph-level embeddings are desired.