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Related Experiment Video

Updated: Jan 7, 2026

In vivo Clonal Tracking of Hematopoietic Stem and Progenitor Cells Marked by Five Fluorescent Proteins using Confocal and Multiphoton Microscopy

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

Kevin Bigott¹, Victoria H Schoppel¹, Manuel Martinez-Osuna¹

¹Miltenyi Biotec B.V. & Co. KG, 51429 Bergisch Gladbach, Germany.

|December 28, 2025

Summary

This study introduces a method for analyzing biomolecules in 3D tissues at high resolution. It combines light sheet imaging with deep cell phenotyping for detailed spatial analysis.

Keywords:

Cancer Microscopy Neuroscience

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Published on: May 11, 2018

Area of Science:

Biological imaging
Tissue analysis
Cellular phenotyping

Background:

Understanding biological processes requires spatial analysis of cells and their microenvironment within tissues.
Analyzing a broad range of biomolecules in large 3D tissue specimens at subcellular resolution is ideal but challenging.

Purpose of the Study:

To present a protocol for identifying and extracting target sections from cleared tissues.
To enable detailed spatial analysis of biomolecules within 3D tissue specimens.

Main Methods:

Protocol for section identification and extraction from cleared tissues.
Combination of 3D light sheet imaging.
3D-guided deep cell phenotyping using multi-cyclic 2D microscopy.

Main Results:

Successful identification and extraction of target tissue sections.
Integration of 3D imaging with advanced cell phenotyping.
High-resolution spatial analysis of biomolecules within tissues.

Conclusions:

The presented protocol facilitates detailed spatial analysis of biomolecules in 3D tissues.
This approach enhances understanding of cellular microenvironments and biological processes.
Combines advanced imaging and phenotyping for comprehensive tissue analysis.