Three-dimensional single-cell transcriptome imaging of thick tissues

Elife. 2024 Dec 27:12:RP90029. doi: 10.7554/eLife.90029.

Abstract

Multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows genome-scale imaging of RNAs in individual cells in intact tissues. To date, MERFISH has been applied to image thin-tissue samples of ~10 µm thickness. Here, we present a thick-tissue three-dimensional (3D) MERFISH imaging method, which uses confocal microscopy for optical sectioning, deep learning for increasing imaging speed and quality, as well as sample preparation and imaging protocol optimized for thick samples. We demonstrated 3D MERFISH on mouse brain tissue sections of up to 200 µm thickness with high detection efficiency and accuracy. We anticipate that 3D thick-tissue MERFISH imaging will broaden the scope of questions that can be addressed by spatial genomics.

Keywords: MERFISH; brain; genome-scale imaging; mouse; neuroscience; spatial genomics; spatial transcriptomics; thick-tissue imaging.

MeSH terms

  • Animals
  • Brain* / diagnostic imaging
  • Gene Expression Profiling / methods
  • Imaging, Three-Dimensional* / methods
  • In Situ Hybridization, Fluorescence* / methods
  • Mice
  • Microscopy, Confocal* / methods
  • Single-Cell Analysis* / methods
  • Transcriptome*

Associated data

  • Dryad/10.5061/dryad.w0vt4b922

Grants and funding

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.