REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-human pan-cytokeratin (AF488)	BioLegend	RRID: AB_2616664
Anti-human CD4 (AF488)	R&D systems	RRID: AB_2728839
Anti-human CD14 (AF488)	Abcam	RRID: AB_2889158
Anti-human CD68 (FITC)	Santa Cruz	Cat#: sc-20060 FITC
Anti-human NF-kB (AF488)	abcam	Cat#: ab190205
Anti-human vimentin (AF488)	BioLegend	RRID: AB_2650955
Anti-human CD103 (AF488)	abcam	RRID: AB_2884944
Anti-human vinculin (AF488)	Thermo Fisher Scientific	RRID: AB_2574473
Anti-human CD45 (BUV395)	BD Biosciences	RRID: AB_2744400
Anti-human Foxp3 (PE)	Thermo Fisher Scientific	RRID: AB_1944444
Anti-human Ki-67 (PE)	BD Biosciences	RRID: AB_2266296
Anti-human CD45RA (PE)	BioLegend	RRID: AB_314412
Anti-human GATA-3 (PE)	BD Biosciences	RRID: AB_1645330
Anti-human CD8 (PE)	Santa Cruz	RRID: AB_1120718
Anti-human CD20 (PE)	BD Biosciences	RRID: AB_10563904
Anti-human CD45RO (PE)	BioLegend	RRID: AB_314422
Anti-human PD-L1 (PE)	BioLegend	RRID: AB_940368
Anti-human SMA (eFluor570)	Thermo Fisher Scientific	RRID: AB_2573630
Anti-human PD-1 (PE)	BioLegend	RRID: AB_2566065
Anti-human pSTAT3 (PE)	Cell Signaling Technology	RRID: AB_10859889
Anti-human beta-Catenin (PE)	Cell Signaling Technology	RRID: AB_10828097
Anti-human CD133 (PE)	Biolegend	RRID: AB_2632879
Anti-human CD79a (PE)	Biolegend	RRID: AB_1089076
Anti-human Annexin A1 (PE)	abcam	Cat#: ab225512
Anti-human CD57 (PE)	Biolegend	RRID: AB_2562758
Anti-human E-Cadherin (PE)	Cell Signaling	RRID: AB_10950323
Anti-human MUC2 (PE)	Novus	Cat#: 34757PE
Anti-human CD123 (PE)	BioLegend	RRID: AB_314580
Anti-human CD45 (PerCP/Cy5.5)	BioLegend	RRID: AB_893338
Anti-human Ki-67 (PerCP/Cy5.5)	BD Bioscience	RRID: AB_10611574
Anti-human CD20 (PerCP/Cy5.5)	BD Bioscience	RRID: AB_396990
Anti-human CD45RA (PerCP/Cy5.5)	BioLegend	RRID: AB_893357
Anti-human CD56 (PerCP)	Novus	Cat#: 33132PCP
Anti-human CD45RA (BV421)	BioLegend	RRID: AB_10900421
Anti-human CD3	Thermo Fisher Scientific	RRID: AB_149924
Anti-rabbit IgG	Biolegend	RRID: AB_893531
Anti-rabbit IgG	Biolegend	RRID: AB_2563484
Biological samples
Healthy adjacent tissues from colon resections	Molecular Tumor Biology (Prof. Dr. Klaus-Peter Janssen) at the Dept. of Surgery (TUM)	N/A
Biopsies from aHSCT patients	University hospital of Regensburg (Prof. Ernst Holler)	N/A
Colorectal cancer resections	TUM Pathology Department (Dr. Katja Steiger)	N/A
Pancreatic cancer resections	TUM Pathology Department (Dr. Katja Steiger)	N/A
Breast cancer resections	TUM Pathology Department (Dr. Katja Steiger)	N/A
Chemicals, peptides, and recombinant proteins
Hoechst	Thermo Fisher Scientific	Cat#: H3570
Ethanol absolute, 1 % MEK	Carl Roth	Cat#: K928
Ethanol 70%, 1 % MEK	Carl Roth	Cat#: T913
Roticlear	Carl Roth	Cat#: A538
Tween-20	Carl Roth	Cat#: 9127
Tris(hydroxymethyl)aminomethane (TRIS)	Carl Roth	Cat#: 9429
Ethylenediaminetetraacetic acid (EDTA)	Carl Roth	Cat#: X986
Sudan Back B	Sigma Aldrich	Cat#: 199664
True Black	Biotium	Cat#: 23007
Dulbecco's phosphate-buffered saline (DPBS)	PAN-Biotech	Cat#: P04-36050P
Sodium Borohydride	Sigma Aldrich	Cat#: 71320
Hydrogen peroxide (H2O2)	Sigma Aldrich	Cat#: H1009
Deposited data
Code and Dataset for pipeline testing	This publication	https://github.com/SebastianJarosch/ChipCytometry-Image-Processing
Software and algorithms
ImageJ 1.53c	Schindelin et al., 2012	https://imagej.net/software/fiji/
Affinity photo V1.8.3	Serif Europe Ltd. 2020	https://affinity.serif.com/
FlowJo 10	FlowJo LLC	https://www.flowjo.com
Prism 9	Graphpad	https://www.graphpad.com
Aperio ImageScope 12.4	Leica Biosystems	https://www.leicabiosystems.com/de/digitalpathologie/verwaltung/aperio-imagescope/
Scanpy 1.8	Wolf et al. (2018)	https://github.com/theislab/scanpy
Matlab R2018b	Mathworks	https://de.mathworks.com/products/matlab.html
Automated fluorescence signal quantification	This study	Zenodo https://doi.org/10.5281/zenodo.5533411