REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-CD20 (clone EP459Y)	Abcam	Cat#ab198941
Rabbit anti-CD4 (clone EPR6855)	Abcam	Cat#ab196147
Rabbit anti-CD44 (clone EPR1013Y)	Abcam	Cat#ab216647
Rabbit anti-CD45 (clone EP322Y)	Abcam	Cat#ab214437
Mouse anti-CD68 (clone KP1)	Biolegend	Cat#916104
Mouse anti-FOXP3 (clone 206D)	Biolegend	Cat#320102
Rabbit anti-Granzyme B (GRNZB) (clone EPR20129-217)	Abcam	Cat#ab219803
Rabbit anti-Cytokeratin 5 (CK5) (clone EP1601Y)	Abcam	Cat#ab193894
Mouse anti-Cytokeratin 14 (CK14) (clone LL002)	Abcam	Cat#ab212547
Rabbit anti-Cytokeratin 17 (CK17) (clone EP1623)	Abcam	Cat#ab185032
Rabbit anti-Cytokeratin 7 (CK7) (clone EPR1619Y)	Abcam	Cat#ab185048
Rabbit anti-Cytokeratin 8 (CK8) (clone EP1628Y)	Abcam	Cat#ab192467
Mouse anti-Cytokeratin 19 (CK19) (clone A53-B/A2)	Biolegend	Cat#628502
Rabbit anti-E Cadherin (Ecad) (clone EP700Y)	Abcam	Cat#ab201499
Rabbit anti-Androgen Receptor (AR) (polyclonal)	Sigma-Aldrich	Cat#06-680-AF555
Rabbit anti-Estrogen Receptor (ER) (clone EPR4097)	Abcam	Cat#ab205851
Rabbit anti-Progesterone Receptor (PgR) (clone YR85)	Abcam	Cat#ab199455
Mouse anti-HER2 (clone 3B5)	Santa Cruz	Cat#sc-33684
Mouse anti-aSMA (clone 3B5)	Santa Cruz	Cat#sc-32251
Rabbit anti-CD31 (clone EPR3094)	Abcam	Cat#ab218582
Rabbit anti-Vimentin (Vim) (clone D21H3)	Cell Signaling Technology	Cat#9854
Rabbit anti-Collagen I (ColI) (clone EPR7785)	Abcam	Cat#ab215969
Mouse anti-Collagen IV (ColIV) (clone 1042)	ThermoFisher	Cat#51-9871-82
Mouse anti-Lamin A/C (LamA/C) (clone 4C11)	Sigma-Aldrich	Cat#SAB4200236
Rabbit anti-Lamin B1 (LamB1) (clone EPR8985(B))	Abcam	Cat#ab194106
Rabbit anti-Lamin B2 (LamB2) (clone EPR9701(B))	Abcam	Cat#ab200427
Rabbit anti-H3K4me3 (clone C42D8)	Cell Signaling Technology	Cat#11960
Rabbit anti-H3K27me3 (clone C36B11)	Cell Signaling Technology	Cat#5499
Mouse anti-Podoplanin (PDPN) (polyclonal)	Biolegend	Cat#916606
Rabbit anti-Cleaved PARP (cPARP) (clone D64E10)	Cell Signaling Technology	Cat#6894
Rabbit anti-gH2AX (clone EP854(2)Y)	Abcam	Cat#ab195189
Rabbit anti-Ki67 (clone D3B5)	Cell Signaling Technology	Cat#12075
Mouse anti-PCNA (clone PC10	Cell Signaling Technology	Cat#8580
Rabbit anti-pHH3 (clone D2C8)	Cell Signaling Technology	Cat#3465
Rabbit anti-p-S6 (clone D57.2.2E)	Cell Signaling Technology	Cat#3985
Biological samples
Breast cancer tissue array	US Biomax Inc.	BR1201a
Breast cancer tissue array	US Biomax Inc.	BR1506
Breast cancer tissue array	US Biomax Inc.	Her2B
Breast cancer tissue array	Dowsett et al., 2008	T-ATAC-4A
Chemicals, peptides, and recombinant proteins
SlowFade Gold Antifade Mountant with DAPI	Life Technologies	Cat#S36938
Normal Goat Serum (NGS)	Vector Laboratories	Cat#S-1000
Bovine Serum Albumin (BSA)	Sigma-Aldrich	Cat#A7906
Phosphate Buffered Saline (PBS)	Fisher Scientific	Cat#BP39920
Target Retrieval Solution, pH 9	Agilent	Cat#S236784-2
Deposited data
Single-cell feature data (OHSU CyCIF)	This paper	10.5281/zenodo.4908899
Single-cell feature data (Basel IMC)	Jackson et al., 2020	10.5281/zenodo.3518284
Software and algorithms
PhenoGraph	Levine et al., 2015	https://github.com/dpeerlab/phenograph
RESTORE	Chang et al., 2020	https://gitlab.com/Chang_Lab/cycif_int_norm/
Code for analysis and figure generation	This paper	https://gitlab.com/eburling/BCTMA
CuPy	Okuta et al., 2017	https://cupy.dev/
SciPy	Virtanen et al., 2020	https://www.scipy.org/
Grapheno	This paper	https://gitlab.com/eburling/grapheno
NetworkX	Hagberg et al., 2008	https://networkx.org/
Pingouin	Vallat, 2018	https://pingouin-stats.org/
Seaborn	Waskom and the seaborn development team, 2020	https://seaborn.pydata.org/
Holoviews	Rudiger et al., 2019	http://holoviews.org/
Bokeh	Bokeh Development Team, 2020	https://docs.bokeh.org
Matplotlib	Hunter, 2007	https://matplotlib.org/
Napari	Sofroniew et al., 2020	https://napari.org/
RAPIDS	Raschka et al., 2020	https://rapids.ai/
Dask	Dask Development Team, 2016	https://dask.org/
Other
24x50 mm rectangular #1½ cover glass	Corning	Cat#2980-245
24x30 mm rectangular #1½ cover glass	Corning	Cat#2980-243
Slide chambers	Bio-Rad	Cat#SLF0601
Tabletop incubator	Clinical Scientific Equipment Inc.	No. 100
Hybridization incubator	Robbins Scientific	Model 1000
Decloaking chamber	Biocare Medical	Cat#DC2012