For each cell phenotype of interest, the density of that cell type in each sample will be quantified as: $\#\ of\ cells/total\ tissue\ area$ with units of $cells/mm^2$

If a dataset is provided with masks that denote specific areas of interest in each sample (i.e. tumor & stroma masks), then the density of each cell phenotype of interest in each sample for each class of ROI will be quantified as $\#\ of\ cells/total\ area\ of\ ROI\ type$ (where ROI type may be “tumor”, “stroma”, etc).

If a metadata trait specifying cohort definitions is provided, the result of a statistical comparison between groups will also be reported for each of these cell densities:

• For cohort definitions with two groups, the result of a two sample t-test will be reported.
• For cohort definitions with more than two groups, the result of a one-way ANOVA will be reported, with a Tukey’s post-hoc test performed to identify significant pairwise differences following significant ANOVA results.
• All reported p-values will be corrected for multiple hypotheses using a Benjamini-Hochberg correction.