Immunoelectron microscopy: a comprehensive guide from sample preparation to high-resolution imaging

Immunoelectron Microscopy (IEM) is a technique that combines specific immunolabeling with high-resolution electron microscopic imaging to achieve precise spatial localization of biomolecules at the subcellular scale (< 10 nm) by using high-electron-density markers such as colloidal gold and quantum dots. As a core tool for analyzing the distribution of proteins, organelle interactions, and localization of disease pathology markers, it has irreplaceable value, especially in synapse research, pathogen-host interaction mechanism, and tumor microenvironment analysis. According to the differences in labeling sequence and sample processing, the IEM technology system can be divided into two categories: the first is pre-embedding labeling, which optimizes the labeling efficiency through the pre-exposure of antigenic epitopes and is especially suitable for the detection of low-abundance and sensitive antigens; the second is post-embedding labeling, which relies on the low-temperature resin embedding (e.g., LR White, Lowicryl) or the Tokuyasu frozen ultrathin sectioning technology, which can improve the deep-end labeling while maintaining the ultrastructural integrity of the tissue. The accessibility of deep antigens is enhanced while maintaining ultrastructural integrity. The two techniques have significant complementarities: the former has high labeling efficiency but limited cellular structure preservation, while the latter has better tissue structure preservation but needs to balance the problems of resin penetration and antigenic epitope masking. This article provides a systematic analysis of the entire IEM workflow, focusing on the synergistic strategies for fixation and dehydration, experimental method selection, and specific application cases. It also introduces a quantitative analysis framework based on systematic random sampling (SUR) and deep learning algorithms (such as Gold Digger), including FIB-SEM 3D reconstruction (with isotropic resolution reaching 5 nm) and correlative light and electron microscopy (CLEM) multimodal integration strategies for functional-structural co-localization. Through technological innovation and cross-platform integration, IEM is driving the advancement of ultrastructural pathology diagnostics and precision nanomedicine to new heights.