Electron Microscopy

EM Techniques and Services

The Imaging Facility offers a suite of electron microscopy techniques tailored for high-resolution investigation of biological systems. Scanning Electron Microscopy (SEM) provides detailed imaging of cell and tissue surface morphology, while Volume EM (vEM) reconstructs three-dimensional ultrastructure of organelles, cells, and tissues at nanometre resolution. Scanning Transmission EM (STEM) enables transmission-mode imaging of thin sections and stained preparations, delivering structural and compositional insights into cellular and macromolecular assemblies. Correlative Light and Electron Microscopy (CLEM) integrates fluorescence with EM to link molecular localization and dynamic processes with ultrastructural context. Together, these methods support multiscale and multimodal studies of cellular architecture, molecular complexes, and biological interactions.

 

EM Techniques and Services Available:

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Volume EM (vEM)

Volume EM enables 3D reconstruction of biological and material samples at nanometre resolution, revealing ultrastructural detail across large volumes. The facility provides two complementary vEM approaches: Focused Ion Beam SEM (FIB-SEM) and Array Tomography, allowing flexible workflows tailored to research needs.

Focused Ion Beam SEM (FIB-SEM)

  • Combines ion beam milling with SEM imaging for automated serial sectioning
  • Generates isotropic 3D datasets down to 5 nm resolution across 10–100 µm volumes
  • Suited for detailed analysis of organelles, subcellular architecture, and cell–cell interfaces

Array Tomography

  • Combines ultramicrotomy, BSE-SEM, and optional fluorescence imaging
  • Collects serial ultrathin resin sections on coverslips for correlative workflows
  • Enables hierarchical imaging: low-resolution overview followed by targeted high-resolution (3–5 nm) imaging
  • Captures volumes up to 3 mm with anisotropic resolution (3 × 3 × 50 nm)
  • Sections can be reimaged, supporting long-term and iterative studies

Scanning Electron Microscopy (SEM)

The Scanning Electron Microscope (SEM) uses a finely focused electron beam to scan the surface of a specimen, generating high-resolution images of topography and composition. Signals such as secondary electrons (SE) and backscattered electrons (BSE) provide complementary information, revealing fine surface morphology and atomic number contrast.

Applications

  • Surface topography and morphology analysis
  • Elemental contrast imaging
  • Advanced imaging modes:
    • Scanning Transmission EM (STEM)
    • Volume EM (FIB-SEM and Array Tomography)

Instrumentation

  • Zeiss Crossbeam 550 SEM equipped with:
    • Everhart-Thornley and inlens SE detectors for high-resolution surface imaging
    • BSD and inlens eBSD detectors for compositional imaging with BSE
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Scanning Transmission Electron Microscopy (STEM)

STEM in SEM provides transmission-mode imaging of electron-transparent specimens, including thin films, ultrathin resin sections, and negatively stained suspensions. Operating at 20–30 kV, it delivers enhanced contrast for low-Z and low-density materials while minimizing beam-induced damage, charging, and contamination compared to conventional TEM (100–300 kV). This technique enables high-resolution structural and compositional analysis of complex samples.

Applications

  • Cellular ultrastructure
  • Macromolecular assemblies
  • Viral morphology

Instrumentation

  • STEM detector with:
    • Brightfield (BF) mode
    • Darkfield (DF) mode
    • High-angle annular darkfield (HAADF) mode

Correlative Light and Electron Microscopy (CLEM)

CLEM integrates light microscopy (LM) with electron microscopy (EM) to combine molecular specificity with ultrastructural resolution. This approach enables comprehensive analysis of cells, tissues, and small organisms by linking dynamic processes captured with LM to high-resolution ultrastructure provided by EM.

Applications

  • Molecular localization with nanometre-scale structural context
  • Correlation of live-cell imaging with post-fixation ultrastructure (e.g., trafficking, signalling, organelle remodelling)
  • Targeted EM imaging of regions of interest guided by fluorescence markers
  • Enhanced interpretation of complex ultrastructure through molecular assignment
  • Multiscale, multimodal analysis combining LM’s large field of view with EM’s high resolution
  • Single-cell and rare event studies within heterogeneous populations
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