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Unterauer, E.M.* ; Schentarra, E.M.* ; Jevdokimenko, K.* ; Shetab Boushehri, S. ; Marr, C. ; Opazo, F.* ; Fornasiero, E.F.* ; Jungmann, R.*

Protocol for SUM-PAINT spatial proteomic imaging generating neuronal architecture maps in rat hippocampal neurons.

STAR Protoc. 6:103637 (2025)

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To unravel the complexity of biological processes, it is necessary to resolve the underlying protein organization down to single proteins. Here, we present a protocol for secondary label-based unlimited multiplexed DNA-PAINT (SUM-PAINT), a DNA-PAINT-based super-resolution microscopy technique that is capable of resolving virtually unlimited protein species with single-protein resolution. We describe the steps to prepare neuronal cultures, troubleshoot and conduct SUM-PAINT experiments, and analyze the resulting feature-rich neuronal cell atlases using unsupervised machine learning approaches. For complete details on the use and execution of this protocol, please refer to Unterauer et al.¹.

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Publication type Article: Journal article

Document type Scientific Article

Corresponding Author

Keywords Cell Biology ; Cell Culture ; Microscopy ; Neuroscience; Microscopy

e-ISSN 2666-1667

Journal STAR Protocols

Quellenangaben Volume: 6, Issue: 1, Article Number: 103637

Publisher Elsevier

Publishing Place Radarweg 29, 1043 Nx Amsterdam, Netherlands

Non-patent literature Publications

Reviewing status Peer reviewed

Institute(s) Institute of AI for Health (AIH)

Grants BMBF
Max Planck Foundation
Max Planck Society
IMPRS-ML graduate school
Deutsche Forschungsgemeinschaft (DFG)
CZI collaborative pair grant
Collaborative Research Center 1286 on Quantitative Synaptologie , Gottingen, Germany
F. Hoffmann-La Roche LTD
European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program
Helmholtz Association under the joint research school "Munich School for Data Science-MUDS"

European Research Council through an ERC Consolidator Grant (ReceptorPAINT)