The Microscope
I.A. Principles of the Transmission Electron Microscope (TEM)
I.A.1 Origin of the Transmission Electron Microscope
I.A.2. Comparison Between Electron And Light Microscopy
I.A.3. Photons/Electrons
I.A.4. Optics (Lens Theory)
I.A.5. Electron Optics
I.B. Design of the Electron Microscope
I.B.1. Electron Gun
I.B.2. Condenser Lenses
I.B.3. Lens Aberrations and other non-ideal imaging properties
I.B.4. Objective Lens and Specimen Stage
I.B.5. Projector Lens (TBD)
I.B.6. Camera and Viewing System (TBD)
I.B.7. Vacuum System (TBD)
I.B.8. Electrical System (TBD)
I.C. Contrast and Image Formation
I.C.1. Electron Scattering
I.C.2. Amplitude/Phase Contrast
I.C.3. Phase Contrast Transfer Theory
I.C.4. Multiple Scattering in Thick Specimens
I.C.5. Other Methods in Enhancing Contrast
I.D. Microcope Disturbances and Alignment
I.D.1 Introduction
I.D.2 Alignment of the Microscope
I.D.3. Disturbances to Microscope Performance
I.E. Operation of the Transmission Electron Microscope
I.E.1. Choice of Accelerating Voltage
I.E.2. Choice of Apertures
I.E.3. Specimen Stage/Holder
I.E.4. Choice of Magnification
I.E.5. Focusing
I.E.6. Magnification Calibration
I.E.7. Resolution Tests
I.E.8. Microscope Maintenance
I.E.9. Microscope Maintenance
I.E.10. Photography
I.F. Other Modes of Transmission Electron Microscope Operation
I.F.1. Electron Diffraction
I.F.2. Dark Field Microscopy
I.F.3. High Resolution Transmission Electron Microscopy
I.F.4. Tilting and Stereo Microscopy
I.F.5. Low Temperature
I.F.6. Energy Loss
I.F.7. X-ray Microanalysis
The Specimen
II.A. Biological Specimen Preparation Techniques
II.A.1. Support Films
II.A.2. Thin Sectioning (Fixation/Dehydration/Embedding/Staining)
II.A.3. Negative Staining
II.A.4. Metal Shadowing
II.A.5. Unstained Specimens
II.A.6. Freeze Drying/Etching/Fracture
II.A.7. Autoradiography
II.B. Radiation Effects
II.B.1. Introduction
II.B.2. Dose/Dose Rate
II.B.3. Primary Effects of Radiation Damage to Biological Specimens
II.B.4. Secondary Effects of Radiation Damage
II.B.5. Ways to Measure Damage/Critical Dose
II.B.6. Procedures to Reduce Radiation Damage
II.B.7. Relation betwen Contrast, Resolution and Radiation Damage
II.B.8. Radiation Effects in Negatively-Stained Specimens
II.B.9. Radiation Effects in Frozen-Hydrated Specimens
The Micrograph
III.A. Introduction to Image Analysis and Processing of Biological Specimens
III.A.1. Image Processing Techniques: Real and Reciprocal Space Methods
III.A.2. Fourier Image Processing
III.A.3. Periodic/Non-Periodic Specimens
III.A.4. Applications and Advantages of Image Processing
III.B. Sources of Noise in TEM Images of Biological Specimens
III.B.1. Specimen Support Film
III.B.2. Specimen
III.B.3. Microscope
III.B.4. Photography
III.C. Crystals, Symmetry, and Diffraction
III.C.1. Definition of Terms
III.C.2. Crystals
III.C.3. Lattices
III.C.4. Crystal Structure
III.C.5. Symmetry
III.C.6.Diffraction
III.D. Fourier Image Processing Techniques
III.D.1. Optical Diffraction
III.D.2. Optical Filtering
III.D.3. Digital Fourier Analysis of Electron Micrographs
III.E. Analyzing Images of Specimens of Different Types
III.E.1.Planar specimens (two-dimensional sheets)
III.E.2. Three-Dimensional Crystals
III.E.3. Particles with Rotational Symmetry
III.E.4. Helical
III.F. Considerations Concerning Specimen Preparation and Microscopy
III.F.1. Sample Preparation
III.F.2. Imaging Conditions
III.G. Image Analysis Using Real Space and Other Reconstruction Methods
III.H. Interpretation and Display of Image Analysis Results
References
Acknowledgments & Future Directions
