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This repo contains the Xenium raw data, code and output files generated for the analysis of the spatial sequencing included in the publication: C1q and immunoglobulins mediate activity-dependent synapse loss in the adult brain. Gerard Crowley et al. This analysis has been performed by ElectrOmics team led by PhD Luca Giudice in Tarja Malm research group. Legend: Each "output-XETG00363*" contains the Xenium raw data of a sample. This folder is the input of the analysis code op1. "Data" contains sample sheet and other meta-information which are needed by the op* in the code folder. "Code" contains the python operations performed on the data, the operations are ordered, op1, op2, op3, etc ... Each operation produces the output needed for the next operation. The same code files have been organized in a github repo: https://github.com/ElectrOmics/Ger_Plasma_Xenium_scRNA_2025 "Output_finals_h5ad" contains the last anndata in h5ad files produced by the analysis such that all the cells' and genes' metrics are accessible (spatial coordinates, t-sne coordinates, pca coordinates, labels, samples' meta-information, etc ...). There is a more detailed legend in the folder that describes each file. "Code_external" contains one R script needed to extract the B cells markers from the external Tabula Muris dataset. Important note, the analysis operations rely on the paths to the data folders, so you have to edit that paths (pointing to the files that you are downloading from this repo in your system) in order to re-run the code.