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Course Outline

Concept Check Questions for all Parts [PDF]


Part 1: Currents, coils, knobs and names: Basic anatomy of the electron microscope
8 modules, ~2 hours total

  • Electron guns
  • EM lenses
  • The column, knobs and names
  • The sample chamber
  • Energy filters
  • Detectors
  • Vacuum systems
  • Summary, safety

 Part 2: Fourier transforms and reciprocal space for beginners
6 modules, ~2 hours total

  • One dimensional waves and sums
  • One-dimensional reciprocal space
  • Two-dimensional waves and images
  • Two-dimensional transforms and filters
  • Three-dimensional waves and transforms
  • Convolution and cross-correlation

 Part 3: Image formation
6 modules, ~3 hours total

  • Amplitude and phase contrast, scattering
  • Wave propagation and phase shifts
  • The contrast transfer function
  • Defocus and its effects
  • Envelopes
  • CTF correction

Part 4: Fundamental challenges in biological EM
5 modules, ~1 hour total

  • Sample prep: Room temperature methods
  • Sample prep: Freezing methods
  • Sample prep: Grids
  • 3-D reconstruction
  • Dose limitations

Part 5: Tomography
5 modules, ~2 hours total

  • Introduction to tomography
  • Data collection and reconstruction
  • Identifying objects of interest
  • Limitations

Part 6: Single-particle analysis
6 modules, ~3 hours total

  • Introduction to single particle analysis
  • Special sample prep issues
  • Data collection (imaging)
  • Reconstruction basics
  • Reconstruction: additional topics
  • Interpretation and limitations

Part 7: 2-D crystallography
4 modules, ~1 hour total

  • Introduction to 2-D crystallography and special sample prep issues
  • The Fourier transform of a 2-D crystal
  • Data collection and reconstruction
  • Helical tubes