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Peer-reviewedCC BY-NC-ND 4.0STAR Protocols

Protocol for 3D-guided sectioning and deep cell phenotyping via light sheet imaging and 2D spatial multiplexing

  • Kevin Bigott
  • Victoria H Schoppel
  • Manuel Martinez-Osuna
  • Leon Osinski
  • Marie-Catherine Tiveron
  • Daniel Barleben
  • Simon F Bornemann
  • Harold Cremer
  • Christoph Herbel
  • Andreas Bosio
  • Melanie Jungblut
Open at sourcePDFDOICite

Abstract

Spatial analysis of cells and their microenvironment within tissues enhances our understanding of biological processes. Ideally, a broad range of biomolecules should be analyzed in large 3D tissue specimens at subcellular resolution. Here, we present a protocol to identify and extract target sections from previously cleared tissues. We describe steps for combining 3D light sheet imaging and sub- sequent 3D-guided deep cell phenotyping via multi-cyclic 2D microscopy

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Cite

BibTeXRIS
BibTeX
@article{bigott2026protocol,
  title = {{Protocol for 3D-guided sectioning and deep cell phenotyping via light sheet imaging and 2D spatial multiplexing}},
  author = {Kevin Bigott and Victoria H Schoppel and Manuel Martinez-Osuna and Leon Osinski and Marie-Catherine Tiveron and Daniel Barleben and Simon F Bornemann and Harold Cremer and Christoph Herbel and Andreas Bosio and Melanie Jungblut},
  journal = {STAR Protocols},
  year = {2026},
  month = oct,
  doi = {10.1016/j.xpro.2025.104296},
  url = {https://hal.science/hal-05795744v1},
  note = {CC BY-NC-ND 4.0},
}
RIS
TY  - JOUR
TI  - Protocol for 3D-guided sectioning and deep cell phenotyping via light sheet imaging and 2D spatial multiplexing
AU  - Kevin Bigott
AU  - Victoria H Schoppel
AU  - Manuel Martinez-Osuna
AU  - Leon Osinski
AU  - Marie-Catherine Tiveron
AU  - Daniel Barleben
AU  - Simon F Bornemann
AU  - Harold Cremer
AU  - Christoph Herbel
AU  - Andreas Bosio
AU  - Melanie Jungblut
PY  - 2026
DA  - 2026/10/12
JO  - STAR Protocols
DO  - 10.1016/j.xpro.2025.104296
UR  - https://hal.science/hal-05795744v1
AB  - Spatial analysis of cells and their microenvironment within tissues enhances our understanding of biological processes. Ideally, a broad range of biomolecules should be analyzed in large 3D tissue specimens at subcellular resolution. Here, we present a protocol to identify and extract target sections from previously cleared tissues. We describe steps for combining 3D light sheet imaging and sub- sequent 3D-guided deep cell phenotyping via multi-cyclic 2D microscopy
SN  - 2666-1667
ER  -