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Related Experiment Video

Updated: May 9, 2026

Single-Cell Resolution Three-Dimensional Imaging of Intact Organoids
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Three-dimensional single-cell transcriptome imaging of thick tissues.

Rongxin Fang1, Aaron Halpern1, Mohammed Mostafizur Rahman2

  • 1Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Center for Brain Science, Harvard University, Cambridge, United States.

Elife
|December 27, 2024
PubMed
Summary
This summary is machine-generated.

Multiplexed error-robust fluorescence in situ hybridization (MERFISH) now images thick tissues in 3D. This advanced spatial genomics technique enhances RNA detection in intact samples up to 200 µm.

Keywords:
MERFISHbraingenome-scale imagingmouseneurosciencespatial genomicsspatial transcriptomicsthick-tissue imaging

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Area of Science:

  • Molecular Biology
  • Genomics
  • Microscopy

Background:

  • Multiplexed error-robust fluorescence in situ hybridization (MERFISH) enables genome-scale RNA imaging in single cells within intact tissues.
  • Current MERFISH applications are limited to thin tissue samples (~10 µm).

Purpose of the Study:

  • To develop and validate a three-dimensional (3D) MERFISH method for imaging thick tissue samples.
  • To expand the capabilities of spatial genomics for analyzing intact biological systems.

Main Methods:

  • Developed a 3D MERFISH protocol optimized for thick samples (up to 200 µm).
  • Utilized confocal microscopy for optical sectioning.
  • Incorporated deep learning to improve imaging speed and quality.

Main Results:

  • Successfully demonstrated 3D MERFISH on mouse brain tissue sections up to 200 µm thick.
  • Achieved high detection efficiency and accuracy in thick samples.
  • The method enables high-resolution RNA imaging in 3D within intact tissues.

Conclusions:

  • The developed 3D MERFISH method significantly expands the applicability of MERFISH to thicker biological samples.
  • This advancement is expected to broaden the scope of spatial genomics research, enabling new biological questions to be addressed.