REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-P16	Roche/Ventana	Cat#705-4793; RRID: AB_2833232
Mouse monoclonal anti-P53	Roche/Ventana	Cat#760-2542; RRID: N/A
Rabbit monoclonal anti-Ki67	Roche/Ventana	Cat#790-4286; RRID: AB_2631262
Mouse monoclonal anti-CK5/6	Roche/Ventana	Cat#790-4554; RRID: AB_2861320
Rabbit monoclonal anti-Her2	Roche/Ventana	Cat#790-2991; RRID: AB_2335975
Mouse monoclonal anti-P63	Biocare Medical	Cat#PM163AA; RRID: AB_10582857
Mouse monoclonal anti-GATA3	Biocare Medical	Cat#CM405B; RRID: N/A
Mouse monoclonal anti-CK20	Cell Marque	Cat#320M-18; RRID: AB_1158255
Rabbit monoclonal anti-CyclinD1	Roche/Ventana	Cat#790-4508; RRID: AB_2335988
Biological samples
H&E and IHC tissue microarrays - Discovery cohort	Johns Hopkins University School of Medicine	N/A
H&E tissue microarray - Validation cohort	University Hospital Bern	N/A
Deposited data
GitHub	Raw features	https://github.com/popellab/MIBC-Predictive-models/tree/Code
Mendeley Data	Performance evaluations of segmentation and classification algorithms	https://doi.org/10.17632/v7xh2m76tw.1
Software and algorithms
QuPath (version 0.2.0-m12)	Bankhead et al.16	https://qupath.github.io/
MATLAB (verson 2020a)	MathWorks	https://www.mathworks.com/products/matlab.html
R (version 3.5.3)	CRAN	https://www.r-project.org/
RStudio desktop (version 1.4)	RStudio	https://www.rstudio.com/
Python (version 3.8)	Python Software Foundation	https://www.python.org/
Pycharm Python IDE (version 2020.3.3)	JetBrains	https://www.jetbrains.com/pycharm/
StarDist	Schmidt et al.18	https://github.com/stardist/stardist
https://github.com/popellab/MIBC-Predictive-models/tree/Code	Analysis code	N/A
Prism (version 9.0.0)	GraphPad Software	https://www.graphpad.com/scientific-software/prism/
BioRender	BioRender	https://biorender.com/
Adobe Photoshop CC (2020)	Adobe	https://www.adobe.com/