Week 1: Objectives and basic working principles of different types of microscopes, including all the light microscope. Different types of electron microscopies, like SEM, TEM, STEM, HT-TEM and their applications.
Week 2: Basic introduction of electron microscopy physics like electron gun (sources), electromagnetic lenses system.
Week 3: Various types of aberrations of lenses (Spherical aberration, Chromatic aberration, Astigmatism, Coma), resolution limit of the microscope, magnification, and diffraction by electron microscope.
Week 4: Microscope basic vacuum system, and camera (CCD & Direct electron detectors). Principles of image formation, Ray diagram to understand the image formation, Fourier analysis.
Week 5: Contrast Transfer Function and point spread function, electron scattering, phase contrast, electron–specimen interactions, electron diffraction.
Week 6: Study the various advanced sample preparation techniques for TEM. Negative staining TEM analysis of soluble protein, membrane protein, DNA-protein complex, RNA-protein complex, lipid-protein complex, liposome sample preparation and imaging and image analysis. Identify good and bad negative staining images.
Week 7: Cryo-EM sample preparation (grid preparation) using Vitrobot, VitroJet, Chameleon and other techniques; We will learn sample preparation and imaging of soluble protein, membrane protein, DNA-protein, lipidprotein. Sample loading and automatic data collection and data analysis.
Week 8: Sample preparation using ultramicrotomes & cryo-ultramicrotomes-- tissue sample, whole cells, polymer, and nanoparticles.Learn the methodology to transfer the thin sections to transfer to grids and visualize and analyze samples using TEM and cryo-EM.
Week 9: Data collection using cryo-EM. Study ray diagram to understand focus overfocus under focus image collection, importance of defocused data collection/image collection (for 3D reconstruction and only for imaging), electron dose rate, identify good and bad image, understand Signal/Noise ratio.
Week 10: Theoretical, computational and practical aspects of various advanced 3D image processing techniques for all kinds of EM data. Basic understanding of Cross-Correlation and Convolution. Describe whole pipeline of 3D reconstruction and importance of 2D classification, 3D classifications.
Week 11: Basic principle behind 3D reconstruction and reference-free 2D classification, 3D classifications. Resolution and FSC calculation.
Week 12: Cryo-EM map interpretation and data analysis, FSC calculation, validation, molecular rigid-body docking and basic of model building.
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