Further explanation of q05_cell_abundance_w_sf values

Thanks for developing such a wonderful tool.

This may be a very stupid question but I wanted some clarifications on q05_cell_abundance_w_sf, it is not clear to me what the meaning of this q05_cell_abundance_w_sf is. Is it relative or absolute cell type abundance? In the tutorials you said that it is the expected number of cells at every spatial location but What does it mean to have values ranging from 0 to 0,2 for a cell type? or 0 to 10? I don’t understand as the maximum amount of cells by spot is 5. Could you explain a little more these amounts?

Thanks in advance!

q05_cell_abundance_w_sf is the absolute cell abundance - the expected number of cells that express every reference cell type signature. So these values range from 0 to arbitrary positive values - there is no maximum number of cells per spot specified anywhere in the model. The expected cell abundance N_cells_per_location is the average total number of cells expected in the tissue. This value is used to guide (prior) cell abundance estimation - not a hard constraint.

In general, the statement “relative cell type abundance” doesn’t have a clear meaning. You need to specify what exactly is computed and presented - eg how the values are normalised. For example, relative cell abundance could mean normalised by tissue area or normalised by volume - a number we present when analysing data types with variable location sizes - such as Nanostring data.

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