Three-dimensional single-cell transcriptome imaging of thick tissues.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 39727221.
- Also identified by DOI 10.7554/eLife.90029 and PMC identifier 11677232.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.
Medical subject headings
- In Situ Hybridization, Fluorescence
- Single-Cell Analysis
- Imaging, Three-Dimensional
- Brain
- Microscopy, Confocal
- Transcriptome