What already happened
before the T cells came
Immunology usually starts with T cells. But it takes days for a T cell to reach a tumour, and much of the outcome is decided before then.
NK cells respond within hours, without ever having learned. Their rule is the opposite of a T cell's: they kill not because something looks wrong, but because the normal signal is missing. Dendritic cells pick up antigen and walk to the lymph node to wake the T cells.
Not just in words: you open 11,128 mouse tumour immune cells and verify the labels, recover the rare cell type the mean had erased, measure cytolytic activity across 10,000 TCGA tumours, and count whether dendritic cells really sit next to NK cells.
How you'll learn
We never re-label the cells — the neighbouring course's clustering stands. Instead we check it every time: is Ncr1 high only in NK, Siglech only in pDC, Ccr7 only in mature DC?
The mean of Xcr1, a cDC1 marker, is 0.008 — it looks absent. Count cell by cell and there are 149 of them. Means erase rare populations.
Lesson 14 permutes cells; lesson 15 permutes mice. Same data, different question. And with only four mice you count out that the smallest attainable p-value is 0.25.
Lesson 18 states a prediction — if the loop runs, NK and DC must sit close together — and lesson 19 checks it against Xenium coordinates. All four samples come out above chance.