(ch:introduction)=
# From Physical Principles to Biological Discovery
Biological electron microscopy reveals the molecular machinery of life well beyond the resolution of light microscopy. _Foundations of Biological Electron Microscopy_ is an interactive textbook designed to guide undergraduate and graduate students through how electron microscopy (EM) is used to study biological structures across scales—from individual proteins to entire cells and tissues. Covering all major EM modalities—transmission, scanning, volume, and correlative techniques—this textbook builds a unified framework that connects physical principles of electron microscopy with modern biological applications that illuminate life's foundational processes at the nanoscale.

The textbook begins by reviewing and establishing essential background knowledge in optics, electromagnetism, and quantum mechanics. You will explore concepts such as lens design, aberrations, diffraction limits, electric and magnetic fields, and Fourier transforms. These principles form the foundation for understanding image formation, signal generation, and resolution in all electron microscopy techniques.

We discuss the basic anatomy of electron microscopes including electron sources, electrostatic/electromagnetic lenses, apertures, electron detectors and filters. We examine the physics of electron–matter interactions, explain how contrast arises from electron scattering and what types of information can be extracted from biological specimens. 

Sample preparation is a critical aspect of biological electron microscopy and we introduce typical sample preparation workflows ranging from chemical fixation and embedding to cryogenic preservation, sectioning, staining, and labelling. We also cover practical considerations for biological imaging such as sample conductivity, thickness, and sensitivity to electron radiation.

We then explore the core modalities of electron microscopy, including transmission (TEM), scanning (SEM), and their advanced extensions including cryo-electron microscopy (cryo-EM), cryo-electron tomography (cryo-ET), volume EM approaches like array tomography and serial block-face imaging and correlative techniques combining fluorescence and electron microscopy. 

Finally, we delve into 3D reconstruction techniques such as single-particle analysis, tomography and subtomogram averaging, explaining the mathematical and computational principles behind generating three-dimensional volumes from two-dimensional projections.