Spatial Profiling of the renal host-pathogen interplay in response to Candida albicans infection in mice

Registration of immunofluorescence slides with spatial transcriptomics visium and identifying pathogens near spots.

This is a project I worked on while at BioImage Informatics Unit, National Bioinformatics Infrastructure Sweden and SciLifeLab. The goal of the was to register three consecutive fluorescently labelled slides between them and with H&E staining as well as spatial transcriptomics slide. The pathogen was to be detected in the fluorescently labelled slides and then their spatial information was included in the spatial transcriptomics data. The project was delivered as a repository with Python scripts and notebooks to run the pipeline.