Table 1.

A sequential decision process was used for generating labels for the 14 nucleus classes from MxIF. The bottom rows show final annotations for the 14 classes.

Step	Purpose	Stain Combinations
1	Group Epi+ nuclei	NaKATPase+ or PanCK+ or Muc2+ or CgA+
2	Group Stroma+ nuclei	Vimentin+ or SMA+
3	Exclude nuclei that are both Epi+ and Stroma+	Exclude nuclei that are marked as (Epi+ and Stroma+)
4	Group Immune+ nuclei	Group nuclei that are CD45+ or CD20+ or CD68+ or CD11B+ or Lysozyme+ or CD3d+ or CD8+ or CD4+
5	Remove immune conflicts for macrophage nuclei across all nuclei	Exclude nuclei where (CD68+ and CD3d+), (CD68+ and CD20+), (CD68+ and CD4+), (CD68+ and CD8+), or (CD68+ and CD11B+)
6	Remove immune conflicts for monocyte nuclei across all nuclei	Exclude nuclei where (CD11B+ and CD3d+), (CD11B+ and CD20+), (CD11B+ and CD4+), (CD11B+ and CD8+), or (CD11B+ and CD68+)
7	Remove immune conflicts for B cell nuclei across all nuclei	Exclude nuclei where (CD20+ and CD3d+), (CD20+ and CD4+), or (CD20+ and CD8+)
8	Remove conflicts for helper T and cytotoxic T nuclei across all nuclei	Exclude nuclei where (CD3d− and CD45− and CD4+), (CD3d− and CD45− and CD8+), or (CD4+ and CD8+)
9	Group Progenitor+ nuclei	Sox9+ or OLFM4+
10	Exclude nuclei that are not in either the epithelium or stroma	Exclude nuclei that are (Epi− and Stroma−)
11	Remove conflicts for goblet cells across all nuclei	Exclude nuclei where (Muc2+ and Immune+), (Muc2+ and Progenitor+), or (Muc2+ and SMA+)
12	Remove conflicts for endocrine nuclei across all nuclei	Exclude nuclei where (CgA+ and Immune+), (CgA+ and SMA+), (CgA+ and Progenitor+), or (CgA+ and Muc2+)
13	Remove conflicts for fibroblasts across all nuclei	Exclude nuclei that are (SMA+ and Immune+)
14	Remove conflicts for progenitors across all nuclei	Exclude nuclei where (Immune+ and Progenitor+)
15	Remove nuclei that are negative for all the large groupings	Exclude nuclei where (Epi− and Stroma− and Progenitor− and Immune−)
16	Remove any immune nuclei from Epi+ group	Exclude Epi+ nuclei where (Epi+ and Immune+)
17	Final annotation for goblet cells	Group Epi+ nuclei where (Muc2+ and Progenitor−)
18	Final annotation for endocrine cells	Group Epi+ nuclei where (CgA+ and Progenitor−)
19	Final annotation for epithelial cells	Group Epi+ nuclei where (CgA− and Progenitor− and Muc2−)
20	Group stromal/fibroblasts	Group nuclei that are Stroma+ and Immune−
21	Final annotation for fibroblasts	Group stromal/fibroblast nuclei where (SMA+ and Progenitor−)
22	Final annotation for stromal nuclei	Group stromal/fibroblast nuclei where (SMA− and Progenitor−)
23	Final annotation for myeloid nuclei	Group Immune+ nuclei that are ((Lysozyme+ and CD68− and CD11B− and Progenitor− and CD20−) and CD3d− and CD8− and CD4−))
24	Final annotation for helper T nuclei	Group Immune+ nuclei where (CD4+ and Progenitor−)
25	Final annotation for cytotoxic T nuclei	Group Immune+ nuclei where (CD8+ and Progenitor−)
26	Final annotation for T cell receptors	Group Immune+ nuclei where (CD3d+ and CD4− and CD8−)
27	Final annotation for monocyte nuclei	Group Immune+ nuclei where (CD11b+ and CD3d− and Progenitor− and CD4− and CD8−)
28	Final annotation for macrophage nuclei	Group Immune+ nuclei where (CD68+ and CD3d− and Progenitor− and CD4− and CD8−)
29	Final annotation for B cell nuclei	Group Immune+ nuclei where (CD20+ and CD68− and CD3d− and Progenitor− and CD4− and CD8−)
30	Final annotation for leukocyte nuclei	Group Immune+ nuclei where (CD45+ and CD20− and CD68− and CD3d− and Progenitor− and CD4− and CD8− and CD11B− and Lysozyme−)
31	Final annotation for progenitor nuclei	Group all nuclei that are Progenitor+