Processed data: inferCNV_output_WM4237.zip, inferCNV_output_WM4007.zip - InferCNV-derived CNV profiles for 12 Visium samples of model WM4237 or WM4007. ad_all_human_clustered_cnv_WM4237.h5ad, ad_all_human_clustered_cnv_WM4007.h5ad - AnnData object containing integration, dimensionality reduction and clustering of the inferCNV-derived CNV profiles for 12 Visium samples of model WM4237 or WM4007. ad_all_human_clustered_im_st_WM4237.h5ad, ad_all_human_clustered_im_st_WM4007.h5ad - AnnData object containing integration, dimensionality reduction and clustering of imaging and nuclear morphometric features (output of STQ pipeline) for 12 Visium samples of model WM4237 or WM4007. "_im" for imaging, "_st" for Visium. ad_all_human_clustered_im_ad_WM4237_m.h5ad, ad_all_human_clustered_im_ad_WM4007_m.h5ad - AnnData object containing integration, dimensionality reduction and clustering of imaging and nuclear morphometric features (output of STQ pipeline) for additional H&E slides (non-Visium) of model WM4237 or WM4007. "_im" for imaging, "_m" for Macenko normalization of the H&E slides with STQ. ids_WM4237_AD.txt, ids_WM4007_AD.txt, ids_WM4237_ST.txt, ids_WM4237_ST.txt - list of identifiers of all samples (tissue sections). ad_all_human_clustered_st_WM4237.h5ad, ad_all_human_clustered_st_WM4007.h5ad - AnnData object containing integration, dimensionality reduction and clustering of RNA profiles for 12 Visium samples of model WM4237 or WM4007. CNV_burden_WM4237.csv, CNV_burden_WM4007.csv - Per-spot values of InferCNV-derived CNV burden for samples of models WM4237 or WM4007. ad_all_scaled_filtered_st_WM4237.h5ad, ad_all_scaled_filtered_st_WM4007.h5ad - AnnData objects containing concatenated and pre-processed samples of WM4237 or WM4007. WM4237_3_AD_m-Imaging-STQ.zip, WM4007_3_AD_m-Imaging-STQ.zip - Imaging portion of STQ pipeline output derived from additional (non-Visium) H&E-stained tissue sections of model WM4237 or WM4007. WM4237_ST-Imaging-STQ.tar.gz, WM4007_ST-Imaging-STQ.tar.gz - Imaging portion of STQ pipeline output derived from Visium H&E-stained tissue sections of model WM4237 or WM4007. WM4237-ST-downstream-output.tar.gz, WM4007-ST-downstream-output.tar.gz - ST-downstream-processing pipeline output for Visium samples of model WM4237 or WM4007. WM4237-STQ-sequencing.tar.gz, WM4007-STQ-sequencing.tar.gz - RNA sequencing portion of STQ pipeline output derived from Visium samples of model WM4237 or WM4007. rna-pseudotime-ordered.zip - Pseudotime ordering of RNA profiles of spots for each time point (T0, T1, T2, T3, T4, TC) for samples of models WM4237 and WM4007.