We decided to first split cells by major class. In order to split the data, and to reject many doublets, we trained a classifier to automatically detect the major class of each single cell, as well as classes representing doublets. We first manually annotated clusters to indicate major classes of cells: Neurons, Oligodendrocytes, Astrocytes, Bergman glia, Olfactory ensheathing cells, Satellite glia, Schwann cells, Ependymal, Choroid, Immune, and Vascular. For some of these classes, we distinguished proliferating cells (e.g., Cycling oligodendrocytes, i.e., OPCs). We also manually identified clusters that were clearly doublets between these major classes (e.g., Vascular-Neurons) as well as clusters that were of poor quality.
