Extended Data Fig. 7: Performance of STELLAR on the MERFISH dataset from mouse cortex.

We applied STELLAR to a large-scale mouse primary motor cortex MERFISH dataset consisting of 23 granular cell types from two mice [8]. (a) Annotation accuracy of STELLAR on the MERFISH mouse cortex dataset with different numbers of withheld cell types. Position of scatter plot points is computed as a mean accuracy score across n=5 runs. Error bars are from standard deviation. We randomly removed a number of cell types from the reference set and evaluated STELLAR’s performance by gradually increasing the number of removed cell types. We measured accuracy separately on classes seen in the reference set and classes withheld from the reference set. Performance is evaluated on the reference cell types, novel cell types withheld from the reference set during training, and jointly on all cell types. (b, c) UMAP visualization of MERFISH mouse cortex dataset from mouse used as the test set. Cells are colored according to (b) ground-truth annotations, and (c) STELLAR’s predictions without any withheld cell types.