This repository contains the raw data for the paper Rakaia: interactive discovery of spatial biology at scale- zip bundle raw_xenium_fig_1.zip contains the raw Xenium outputs for Extended Data Fig 1: https://github.com/camlab-bioml/2025-rakaia-paper-analysis/tree/main/extended_data_fig_1 - zip bundle multimodal_integration_fig_1.zip contains both the Xenium morphology focus images and matched IMC ROI to the raw Xenium outputs for the integrated field of view (FOV) in Extended Data Fig 1: https://github.com/camlab-bioml/2025-rakaia-paper-analysis/tree/main/extended_data_fig_1- zip bundle dm_immune_fig_2.zip contains the steinbock IMC pipeline output directory with the raw MCD images and single cell quantification for Main Fig. 2: https://github.com/camlab-bioml/2025-rakaia-paper-analysis/tree/main/fig_2. The predictions for each IMC ROI for hyperplasia are found in the phenotypeSearch column in both dm_immune.h5ad and measurements.csv- zip bundle dm_immune_tiff_fig_2. zip contains the TIFF format of the IMC images in dm_immune_fig_2.zip that appear in Main Fig. 2- More information about the format of the IMC pipeline output can be found here: https://github.com/camlab-bioml/steinbock_snakemake