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Updated: Oct 26, 2025
Optical Clearing and Imaging of Immunolabeled Kidney Tissue
Published on: July 22, 2019
Tissue clearing and 3D imaging - putting immune cells into context
Julian Hofmann1,2, Selina J Keppler1,2
1Institute for Clinical Chemistry and Pathobiochemistry, München rechts der Isar (MRI), Technical University Munich, 81675 Munich, Germany.
Insights
Optical clearing and 3D imaging enable detailed study of immune cells in their natural environments. This review covers methods, challenges, and applications for analyzing immune cell localization and quantification in various tissues.
Area of Science:
- Immunology
- Cell Biology
- Biomedical Imaging
Background:
- Understanding cell-cell and cell-niche interactions is vital for inflammatory and pathophysiological conditions like viral infections, tumor microenvironments, and neuroinflammation.
- Optical clearing and 3D volumetric imaging offer advanced methods for studying cells in their native tissue context.
- Previous applications focused on structural components, but recent advancements allow detailed examination of immune cells within their niches.
Purpose of the Study:
- To review recent developments in tissue clearing and 3D imaging techniques.
- To focus on the localization and quantification of immune cells within their microenvironments.
- To discuss challenges and future directions for immune cell analysis in homeostatic and inflammatory settings.
Main Methods:
- Summarizing recent advancements in optical clearing methodologies.
- Discussing 3D volumetric imaging techniques for large tissue samples or whole organs.
- Reviewing protocols, limitations, and image analysis strategies for immune cell imaging.
Main Results:
- Optical clearing and 3D imaging are powerful tools for visualizing cells in situ.
- These techniques are increasingly applied to study immune cells within specific niches.
- Challenges in imaging and analysis are being addressed to improve resolution and quantification.
Conclusions:
- Tissue clearing and 3D imaging provide unprecedented insights into immune cell behavior and distribution.
- Future developments will enhance the analysis of immune cells in both healthy and diseased states.
- This approach is crucial for understanding complex immune responses in various pathophysiological scenarios.
Abstract:
A better understanding of cell-cell and cell-niche interactions is crucial to comprehend the complexity of inflammatory or pathophysiological scenarios such as tissue damage during viral infections, the tumour microenvironment and neuroinflammation. Optical clearing and 3D volumetric imaging of large tissue pieces or whole organs is a rapidly developing methodology that holds great promise for the in-depth study of cells in their natural surroundings. These methods have mostly been applied to image structural components such as endothelial cells and neuronal architecture. Recent work now highlights the possibility of studying immune cells in detail within their respective immune niches. This Review summarizes recent developments in tissue clearing methods and 3D imaging, with a focus on the localization and quantification of immune cells. We first provide background to the optical challenges involved and their solutions before discussing published protocols for tissue clearing, the limitations of 3D imaging of immune cells and image analysis. Furthermore, we highlight possible applications for tissue clearing and propose future developments for the analysis of immune cells within homeostatic or inflammatory immune niches.
