Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)

• 10x scRNA-seq clustering analysis and annotation: learn about the whole mouse brain taxonomy through some example use cases and visualization. [notebooks/cluster_annotation_tutorial.ipynb]

• 10x scRNA-seq gene expression data: learn about the 10x dataset through some example use cases

• MERFISH whole brain spatial transcriptomics: learn about the MERFISH dataset through some example use cases

• Cluster groups and embeddings: learn about cell types neighborhoods and neighborhood specific UMAP embeddings through example use cases. [notebooks/cluster_groups_and_embeddings_tutorial.ipynb]

• Cell type neighborhood gallery: explore and visualize a set of cell types neighborhoods. [notebooks/cluster_neighborhood_gallery.ipynb]

• Allen CCFv3 parcellation and annotation: learn about the Allen CCFv3 and a simplified 5-level anatomical hierarchy through some example use cases and visualization. [notebooks/ccf_and_parcellation_annotation_tutorial.ipynb]

• MERFISH CCF mapped coordinates: learn about how to download and use CCF mapped coordinates through some example use cases and visualization. [notebooks/merfish_ccf_registration_tutorial.ipynb]