Reviving formalin-fixed, paraffin embedded (FFPE) tissues for on-slide and multiscale correlative microscopy

Area of Science:

• Biomedical Imaging
• Electron Microscopy
• Histology

Background:

• Correlative microscopy combines multiple imaging techniques for comprehensive biological sample analysis.
• Formalin-fixed, paraffin-embedded (FFPE) tissues are abundant clinical archives but often challenging for high-resolution imaging.
• Existing methods may not fully exploit the structural information within FFPE specimens.

Purpose of the Study:

• To present novel correlative microscopy workflows for FFPE human tissues.
• To demonstrate the utility of archived FFPE specimens for multiscale structural analysis.
• To establish FFPE tissues as a valuable resource for advanced imaging in research and clinical settings.

Main Methods:

• Developed an on-slide correlative light and electron microscopy (CLEM) workflow integrating brightfield light microscopy and scanning electron microscopy.
• Established a multiscale 3D workflow combining X-ray micro-computed tomography (micro-CT) and serial block-face scanning electron microscopy (SBF-SEM).
• Applied artificial intelligence (AI)-assisted image processing and segmentation for quantitative analysis of large datasets.

Main Results:

• Demonstrated that FFPE tissues from liver, lung, brain, and heart retain structural integrity for cellular and subcellular resolution.
• Successfully resolved ultrastructural features from standard FFPE histological sections using on-slide CLEM.
• Achieved targeted, volumetric ultrastructural analysis within defined tissue contexts using the multiscale 3D workflow.
• Validated the scalability and quantitative potential of AI-assisted analysis for large imaging datasets.

Conclusions:

• FFPE human tissues are a versatile and accessible resource for multiscale correlative imaging.
• The presented workflows enhance the utility of archived clinical specimens for high-resolution structural analysis.
• These methods facilitate advanced research and clinical applications by enabling detailed examination of tissue architecture.