I have pre-defined phenotypes for my cells from HALO. In usage of SPIAT I do not want the program to set intensities & predict the cell type for me. Is there anyway to read in the phenotypes that have already been assigned instead of having the program assign them based on the cell intensity?

Thanks

This section of the vignette seems to indicate that SPIAT takes the phenotypes directly from HALO.

If you use format_halo_to_spe or format_image_to_spe with parameter format="HALO", the phenotypes would be the ones generated by HALO. If you want to use your own phenotypes, try "general" format instead of "HALO" (see section).