Correlative Light and Electron Microscopy in Cell Biology: Accessible Pre-Embedding and Post-Embedding Strategies

Aleksandar Janev; Urška Dragin Jerman; Mateja Erdani Kreft

doi:10.5566/ias.4011

Authors

Aleksandar Janev University of Ljubljana, Faculty of Medicine
Urška Dragin Jerman University of Ljubljana, Faculty of Medicine
Mateja Erdani Kreft University of Ljubljana, Faculty of Medicine

DOI:

https://doi.org/10.5566/ias.4011

Keywords:

Correlative light and electron microscopy, pre-embedding, post-embedding, correlative imaging, multimodal probes, sample preparation

Abstract

Correlative light and electron microscopy (CLEM) combines the molecular specificity of fluorescence light microscopy with the ultrastructural resolution of electron microscopy (EM), enabling molecularly defined cellular structures to be localised and interpreted within their cellular ultrastructural context. Although cryo-CLEM, super-resolution CLEM, and volume EM have substantially expanded the spatial, molecular, and three-dimensional capabilities of CLEM, their routine implementation remains constrained by specialised instrumentation, demanding sample-preparation workflows, and the need for expertise in image acquisition, registration, and analysis. This review therefore focuses on conventional CLEM strategies that are accessible to laboratories equipped with standard widefield or confocal fluorescence microscopes and transmission electron microscopes. Pre-embedding and post-embedding approaches are compared, highlighting how the timing of labelling and fluorescence imaging influences key trade-offs among live-cell imaging, correlation accuracy, probe preservation, and ultrastructural integrity. Probes used in pre-embedding workflows are further evaluated, including dual-modality probes such as FluoroNanogold antibodies and quantum dots, fluorescent proteins like GFP (rendered EM-visible through secondary immunolabelling or photoconversion), and luminescent metal complexes, alongside selected protocol examples for both pre-embedding and post-embedding experimental approaches. Overall, successful CLEM depends on careful experimental design, appropriate probe selection, and optimised sample preparation. Conventional workflows remain practical and robust options for routine cell biology studies, particularly when accessibility, reproducibility, and compatibility with existing microscopy infrastructure are priorities.

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