I am using the tutorial for multiplexed analysis with my samples and it works very well. My issue is when I try to add tissue segmentation ( Tumor vs stroma) in my WSI using pixel classification, it also works great, however my cell clasification is deleted. I think i am not resolving the hierarchy…My idea would be cell segmentation using stardist, tissue segmentation ( only 3 areas in the WSI: tumor vs stroma and ignore) and cell classification, in order to calculate immune infiltration in the tumor and percentage of immune phenotypes in the stroma
Do you know how I can resolve this hierarchy?
Many thanks for your help