I am wondering how much we can see the correlation between FACS data and tissue staining?
I am counting immune cells in a tumor (xenograft in mouse) using FACS with single cell isolation and also doing IF staining to reveal the distribution of those immune cells in tissue mass. Using ImageJ software I also can count the immune cells on the slice to know how much relatively they have among the total cells (stained with DAPI). Do you have experience or know any paper discussing about this issue?
Thank you and have a nice day ^^
The main problem you will face is the high accuracy of counting by FACS, and the low accuracy by microscopy. If you seriously want to find a correlation, you will likely need to use better software (Aperio offers some good options). If all you are doing is looking at the number of immune cells and their distribution, which you are seem to be doing successfully using FACS and microscopy respectively, then I don't think there is any need to calculate correlations. I would be very surprised if a reviewer would ask you this.
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