This record contains the data and scripts needed to reproduce the analyses in the paper. There are 3 zip files: 1. banksy-Python_scripts.zip This contains a snapshot of the python repo to reproduce the Slide Seq and Starmap analysis, also found at https://github.com/prabhakarlab/Banksy_py/tree/Banksy_manuscript 2. banksy-R_scripts This contains the scripts to reproduce the results of datasets analyzed using R. The following directories can be found within the zip file. - fig3-crc- fig3-hypothalamus- fig4-hippocampus- fig5-dlpfc- suppfig-codex- suppfig-cosmx- artificial-data Note: The scripts in this archive can also be found on the GitHub page: https://github.com/jleechung/banksy-zenodo . Unlike this Zenodo archive, which contains all data files and scripts, the corresponding GitHub repository does not contain the data files (which are large, and therefore not appropriate for hosting there). Instead, it contains instructions for downloading those files. 3. VeraFISH_data_raw_0728_A013_MuBr.zip This contains the VeraFISH raw data.