BodenmillerGroup/imctoolkit

imctoolkit anndata export empty data matrix

Closed this issue · 0 comments

Exporting single-cell data via .to_anndata() creates AnnData objects where cell_channel properties are stored in layers. However the main adata.X data matrix is left empty. This can lead to errors when handling multiple adata export objects from imctoolkit, such as when concatenating multiple adata objects (which returns a shape error).

Might be useful to default load mean intensities into the adata.X?