AI	artificial intelligence
AOIs	areas of illumination
CNBs	core needle biopsies
CT	tumor center
CTA	Cancer Transcriptome Atlas
DCIS	ductal carcinoma in situ
DFS	disease free survival
DSP	Digital Spatial Profiler
ECM	extracellular matrix
ER	estrogen receptor
FFPE	formalin-fixed paraffin-embedded
GBCC	GeoMx Breast Cancer Consortium
GSEA	gene set enrichment analysis
H&E	hematoxylin and eosin
HCA	Human Cell Atlas
HER2	epidermal growth factor receptor 2
HK	housekeeping
HuBMAP	Human Biomolecular Atlas Program
IDC	invasive ductal carcinoma
IgG	immunoglobulin G
IHC	immunohistochemistry
ILC	invasive lobular carcinoma
IM	invasive margin
LCIS	lobular carcinoma in situ
MIAME	Minimum Information About a Microarray Experiment
MINSEQE	Minimum Information About a Next-generation Sequencing Experiment
NGS	next generation sequencing
PanCK	pan-cytokeratin
PCA	principal component analysis
pCR	pathological complete response
PD	pharmacodynamic
PR	progesterone receptor
ROIs	regions of interest
TILs	tumor-infiltrating lymphocytes
TMA	tissue microarray
TME	tumor microenvironment
TMM	trimmed mean of M values
TNBC	triple-negative breast cancer
tSNE	t-distributed stochastic neighbor embedding
UMAP	uniform manifold approximation and projection
UV	ultraviolet
WTA	Whole Transcriptome Atlas