Data that also records
where each cell was
Single-cell RNA-seq tears cells out of the tissue to read them, and in that moment where they were is lost. Xenium spatial transcriptomics reads them with the tissue left intact โ so every cell has x and y coordinates, and so does every single mRNA molecule.
One slice of tumour: 198,792 cells and 95.48 million molecules. These 20 lessons are how you read those coordinates.
How you'll learn
The smallest unit in this data is not a cell but an mRNA molecule. In a single field of view (200ร200 ยตm) you handle the coordinates and quality scores of 356,319 molecules yourself.
You use the DAPI microscope image of that same field, exactly as captured. Overlay the molecules and the cell boundaries on it and what the data means becomes visible at a glance.
Xenium images 649 negative-control probes alongside the real ones. It is one of the rare datasets in which you can compute the false-positive rate yourself.
โHave the T cells got inside the tumour, or are they held at the margin?โ โ you answer questions single-cell data cannot touch and only spatial data can.