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Spatial Transcriptomics-correlated Electron Microscopy

Peter Androvic, Martina Schifferer, Katrin Perez Anderson, Ludovico Cantuti-Castelvetri, Hao Ji, Lu Liu, Simon Besson-Girard, Johanna Knoferle, Mikael Simons, Ozgun Gokce
bioRxiv doi:10.1101/2022.05.18.492475

Current spatial transcriptomics methods identify cell states in a spatial context but lack morphological information. Scanning electron microscopy, in contrast, provides structural details at nanometer resolution but lacks molecular decoding of the diverse cellular states. To address this, we correlated MERFISH spatial transcriptomics with large area volume electron microscopy using adjacent tissue sections. We applied our technology to characterize the damage-associated microglial identities in mouse brain, allowing us, for the first time, to link the morphology of foamy microglia and interferon-response microglia with their transcriptional signatures.