Class Notes

 I. THE MICROSCOPE pgs. 1-114

A. PRINCIPLES OF THE TRANSMISSION ELECTRON MICROSCOPE (TEM) pgs. 1-28

1. Origin of the Electron Microscope pg. 1
2. Comparison of Light and Electron Microscopes pgs. 1-4
3. Photons/Electrons pgs. 5-11
4. Optics pgs. 12-19
5. Electron Beams / Electron Optics / Magnetic and Electrostatic Lenses pgs. 19-28

B. DESIGN OF THE TEM pgs. 29-57

1. Electron gun pgs. 29-32
2. Condenser Lens pgs. 32-35
3. Lens Aberrations pgs. 35-42
4. Objective Lens and Specimen Stage pgs. 42-48
5. Projector Lens pgs. 48-50
6. Camera and Viewing System pgs. 51-52
7. Vacuum System pgs. 52-56
8. Electrical System pgs. 56-57

C. CONTRAST AND IMAGE FORMATION pgs. 58-64

1. Electron Scattering pgs. 58-60
2. Amplitude/Phase Contrast pgs. 60-63
3. Phase Contrast Transfer Function pg. 63
4. Multiple Scattering in Thick Specimens pg. 64
5. Other Methods for Enhancing Contrast pg. 64

D. ALIGNMENT/ADJUSTMENT OF THE TEM pgs. 65-73

1. Introduction pg. 65
2. Alignment of the Microscope pgs. 65-70
3. Disturbances to Microscope Performance pgs. 70-73

E. OPERATION OF THE TEM pgs. 74-93

1. Choice of Voltage pgs. 74-75
2. Choice of Apertures pg. 75
3. Specimen Stage/Holder pg. 75
4. Choice of Magnification pg. 76
5. Focusing pgs. 77-80
6. Magnification Calibration pgs. 80-82
7. Resolution Tests pgs. 82-84
8. Image Intensifier / TV Display pgs. 84-85
9. Microscope Maintenance pgs. 85-86
10. Photography pgs. 86-93

F. OTHER MODES OF TEM pgs. 94-114

1. Electron Diffraction pgs. 94-100
2. Dark Field pgs. 101-106
3. High Resolution pgs. 106-107
4. Tilting and Stereo Microscopy pgs. 107-112
5. Low Temperature pg. 112
6. Energy Loss pgs. 112-113
7. X-ray Microanalysis pgs. 113-114

 II. THE SPECIMEN pgs. 115-174

A. BIOLOGICAL SPECIMEN PREPARATION TECHNIQUES pgs. 115-161

1. Specimen Support Films for TEM pgs. 115-121
2. Thin Sectioning (Fixation/Dehydration/Embedding/Staining) pgs. 121-135
3. Negative Staining pgs. 136-142
4. Metal Shadowing pgs. 143-149
5. Unstained Specimens pgs. 149-155
6. Freeze Drying/Etching/Fracture pgs. 155-158
7. Autoradiography pgs. 158-161

B. RADIATION EFFECTS pgs. 162-174

1. Introduction pg. 162
2. Dose/Dose Rate pg. 162
3. Primary Effects of Radiation Damage to Biological Specimens pgs. 162-164
4. Secondary Effects of Radiation Damage to Biological Specimens pgs. 165-167
5. Ways to Measure Damage/Critical Dose pgs. 167-169
6. Procedures to Reduce Radiation Damage pgs. 170-172
7. Relation Between Contrast, Resolution and Radiation Damage pg. 172
8. Radiation Effects in Negatively-Stained Specimens pgs. 172-174
9. Radiation Effects in Frozen-hydrated Specimens pg. 174

 III. THE MICROGRAPH pgs. 175-253 (Some parts of this section are not currently available)

A. INTRODUCTION TO IMAGE ANALYSIS OF BIOLOGICAL SPECIMENS pgs. 175-176

1. Image Analysis Techniques: Real and Reciprocal Space Techniques pg. 175
2. Fourier Image Processing pgs. 175-176
3. Periodic/Non-Periodic Specimens pg. 176
4. Applications and Advantages of Image Processing pg. 176

B. SOURCES OF NOISE IN TEM IMAGES OF BIOLOGICAL SPECIMENS pg. 177

1. Specimen Support Film pg. 177
2. Specimen pg. 177
3. Microscope pg. 177
4. Photography pg. 177

C. CRYSTALS, SYMMETRY AND DIFFRACTION pgs. 178-216

1. Definition of Terms pgs. 178-179
2. Crystals pg. 179
3. Lattices pgs. 179-181
4. Crystal Structure pgs. 181-182
5. Symmetry pgs. 183-195
6. Diffraction pgs. 195-216

D. FOURIER IMAGE PROCESSING TECHNIQUES pgs. 217-253

1. Optical Diffraction ...
2. Optical Filtering ...
3. Digital Fourier Analysis of Electron Micrographs (4.6MB) pgs. 217-240
4. 2D and 1D Digital Fourier Reconstruction Methods (4.6MB) pgs. 241-253
     Power Point Lecture (2.8MB)

E. ANALYZING IMAGES OF SPECIMENS OF DIFFERENT TYPES

1. Planar Specimens
2. Particles with Rotational Symmetry
3. Helical
4. Three-dimensional Crystals
5. Asymmetric Particles

F. SPECIMEN PREPARATION AND MICROSCOPY

1. Sample Preparation
2. Imaging Conditions

G. REAL SPACE AND OTHER RECONSTRUCTION METHODS H. INTERPRETATION AND DISPLAY OF IMAGE ANALYSIS RESULTS