This is the umbrella archive that contains all the datasets and code associated with: A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids Vito RT Zanotelli Matthias Leutenegger Xiao‐Kang Lun Fanny Georgi Natalie de Souza Bernd Bodenmiller Mol Syst Biol. (2020) 16: e9798 https://doi.org/10.15252/msb.20209798 Please cite this article if you re-use any of the data or code. Datasets: Brightfield plate images: Contains all plate acquisitions for the individual sphere plates before pooling 4 cellline experiment: p173: 10.5281/zenodo.3991929 p176: 10.5281/zenodo.3991931 Overexpression experiment: p161: 10.5281/zenodo.3991925 p165: 10.5281/zenodo.3991927 Slidescan images: Contains all fluorescent slidescan images of the cuts derived from the pooled spheroid sample blocks 4 cellline experiment: p173: 10.5281/zenodo.3991921 p176: 10.5281/zenodo.3991923 Overexpression experiment: p161: 10.5281/zenodo.4066430 p165: 10.5281/zenodo.3991919 Spillover acquisitions: Contains all spillover acquisitions associated with the two experiments: 4 cellline experiment: p173/p176: 10.5281/zenodo.3991945 Overexpression experiment: p161/p165: 10.5281/zenodo.3991947 Imaging mass cytometry acquisitions: 4 cellline experiment: p173: 10.5281/zenodo.3991937 p176: 10.5281/zenodo.3991939 Overexpression experiment: p161: 10.5281/zenodo.3991933 p165: 10.5281/zenodo.3991935 Processed data set: 4 cellline experiment: 10.5281/zenodo.3991942 Overexpression experiment: 10.5281/zenodo.4271917 Code: A snakemake pipeline to reproduce the analyses from this raw data can be found at: http://github.com/BodenmillerGroup/SpheroidPublication A version already containing all the containers can be found at: 10.5281/zenodo.4071861