CellTypist Labeling Models

To enable you to label your own PBMC datasets, we supply models for the CellTypist cell labeling framework. Below are links for each of the 3 cell type resolutions generated for our Healthy Immune Atlas:

Level 1 (AIFI_L1): 9 broad cell classes
Level 2 (AIFI_L2): 29 intermediate resolution cell types
Level 3 (AIFI_L3): 71 high resolution cell types

Here, we provide models that use the full set of 10x Genomics 3' scRNA-seq features, as well as models for use with data generated using the 10x Genomics Single Cell Gene Expression Flex scRNA-seq system, which uses a subset of the genes available for 3' scRNA-seq.

Cell Type Colorset

In addition to our labeling models, we provide the colorsets that we used to generate our scRNA-seq visualizations. These colors were selected in collaboration with Heidi Gustafson, an artist and pigment foraging expert. More information about Heidi's work can be found at https://earlyfutures.com/.