Test dataset for "Spatial Integration of Multi-Omics Data from Serial Sections using the novel Multi-Omics Imaging Integration Toolset"

The uploaded tar file contains anonymized and reduced test data for the paper "Spatial Integration of Multi-Omics Data from Serial Sections using the novel Multi-Omics Imaging Integration Toolset". (doi: https://doi.org/10.1101/2024.06.11.598306; https://github.com/mwess/miit) Dataset description:- 9 serial histology sections with the following stains: (HES, HE, HES, HES, HES, MTS, IHC, IHC, HES)- Sections are indexed in the following way (due to some sections not being part of this project): 1,2,3,6,7,8,9,10,11- Each serial section contains: - landmarks with matching labels across all sections. - semi-manually generated tissue masks - Section 2 contain spatial transcriptomics data and one annotation file in geojson format.- Sections 6 and 7 contain imzml data that were generated with MALDI-MSI in positive ion mode (section 6) and negative ion mode (section 7) and additional histology annotations.- MALDI-MSI is reduced. The positive ion data contains only intensities and spectra for spermine. The negative ion mode data contains only intensities and spectra for citrate and zinc.- ST data contains only locations of spots and scalefactors. (I.e. no count data is included.). Barcode ids are randomly generated. - In addition, for each ST spot histopathological annotations and GSEA scores for the Citrate-Spermine Secretion gene signature are provided. Abbreviations: - HES = Hematoxylin-Erythrosine-Saffron- HE = Hematoxylin-Eosin- MTS = Masson's Trichrome Staining- IHC = Immunohistochemistry- ST = Spatial Transcriptomics, here refers to Visium10X arrays.- MALDI-MSI = Matrix-Assisted Laser Desorption Ionization - Mass Spectrometry Imaging.