This repository contains data from a spatial transcriptomics (ST) analysis of brain tumor cryosections (medulloblastoma with extensive nodularity, MBEN). It is associated with the preprint by Rademacher, Huseynov, Bortolomeazzi et al. 2024, bioRxiv, https://doi.org/10.1101/2024.04.03.586404, that has a full description of the work. In the study four imaging-based ST methods – RNAscope HiPlex, Molecular Cartography, MERFISH/Merscope, and Xenium – as well as sequencing-based ST (Visium) and single cell RNA sequencing of dissociated nuclei (snRNA-seq) were compared. The files provided here are described in readme.txt and include the transcript count matrices acquired on the Visium platform as well as Seurat objects of the data and analysis results for the comparison of the different technologies. The data for snRNA-seq, RNAscope HiPlex and Molecular Cartography included in the Seurat objects are based on the primary data acquired in a previous study (Ghasemi et al. 2024, Nat Commun, https://doi.org/10.1038/s41467-023-44117-x).