labsyspharm
Building neighborhoods
This is more of a question rather than an issue:
I have built my neighborhoods but when I use the function as in the tutrial with 22 phenotypes I find it quite hard to be able to say for example where my TILs are etc.
Could you somehow guide me through this. I also have the 200 different images
This step is typically quite manual. I usually analyze the cellular composition of each neighborhood and overlay the data onto the image to assign meaningful names. For instance, a neighborhood enriched in B cells and T cells would likely correspond to lymphoid aggregates or tertiary lymphoid structures (TLS). In some cases, it may be necessary to merge clusters with similar compositions. If I overlay these merged clusters onto the image and observe that they form ball-like structures, it provides confirmation that they are TLS. This process involves reviewing each cluster individually and naming them based on their cellular composition and spatial localization.
