Course10210866857 lectures
Fundamentals of Cryo-Electron Microscopy (Cryo-EM) and 3D Image Processing in Structural Biology
Prof. Somnath Dutta · IISc Bangalore
About
This course offers a comprehensive and practical introduction to the fundamentals of Cryo-Electron Microscopy (Cryo-EM), designed to help biologists build a strong foundation—from understanding the microscope itself to learning advanced data collection methods and image analysis.
Cryo-EM has become a powerful tool in structural biology, making it easier and more accurate to study complex biomolecules like proteins, large assemblies, and cell organelles.
The course offers focused modules on the anatomy and recent advancements of Cryo-EM systems, incorporating cutting-edge techniques such as CLEM, FIB-SEM, and High-Pressure Freezing. It covers core principles including electron scattering, specimen interactions, and electron diffraction, alongside diverse sample preparation methods. Participants gain practical expertise through virtual hands-on training in plunge freezing, grid optimisation, and automated data acquisition, providing a comprehensive foundation in modern Cryo-EM workflows.
Start your journey into the microscopic world with this exciting course.
Intended audience: UG and PG student
Prerequisites: Students with a basic understanding of science—particularly in biology, physics, or chemistry—are eligible to enroll in this course.
Lectures
Week 1 Introduction to microscope
- Introduction of the microscope
- Image formation by glass lenses and its role in wavelength
- Different components of electron microscope (EM)
- Electron specimen interaction
- Elements of TEM: electron gun - I
Week 2 Components of an electron microscope: electron gun and lens
- Elements of TEM: electron gun - II
- Comparison between the various types of electron gun
- Elements of TEM: electromagnetic lens (EM) - I
- Trajectory of electrons in EM lens
- Elements of TEM: electromagnetic lens (EM) - II
Week 3 Different component of the microscope: imaging procedure, formation and aberration due to lens
- Image Formation by EM Lenses: Understanding Ray Diagrams
- Aberrations and Focusing in Cryo-EM imaging
- Understanding Chromatic, Spherical Aberrations, and Astigmatism in Cryo-EM
- Aberrations and Practical Imaging in Cryo-EM
- Electron Dose Control and Beam Optimization in Cryo-EM
Week 4 TEM imaging system: holder, pumps and camera
- Introduction to TEM Holders and Grids in Cryo-EM
- Overfocused and Underfocused Images
- Elements of TEM: Pumps in EM System
- Elements of TEM: Detectors in EM System
- Imaging and Effect of Thermal Drift
Week 5 Fundamentals of image formation-1D
- Wave and its properties
- Addition/superposition of waves - I
- Addition/superposition of waves - II
- Decomposition of complex waves
- wave and their transformation
Week 6 Sample Preparation and Purification for TEM
- Complex 2D Images & Its Diffraction Pattern
- Sample Preparation & Determination for TEM
- Biological Sample Purification - I
- Biological Sample Purification - II
- Different Sample Preparation Techniques for TEM Imaging & Different Types of Grids used for Imaging
Week 7 TEM Grids, Grid Preparation & Negative Staining Techniques
- TEM Grids: Types, Handling & Surface Coatings
- Carbon Coaters, Glow Discharge & Grid Surface Treatment
- Negative Staining in TEM: Stains, Grid Preparation & Protocols
- Carbon Sandwich & Metal Shadowing Techniques in TEM
- Staining Quality in TEM: Thick, Thin & Positive Staining
Week 8 Negative Staining & its Applications with Ultramicrotomy in TEM
- Negative Staining – Imaging Quality & Artifacts
- Negative Staining – Particle Distribution & Contrast
- Applications of Negative Staining in Structural Biology
- Negative Staining for Complexes and Interactions
- Ultramicrotomy and Sectioning for Biological Molecules
Week 9 Cryo-EM Grid Preparation, Vitrification & Imaging Fundamentals
- Cryo-EM Grid Preparation & Vitrification
- Grid Types & Sample Distribution in Cryo-EM
- Blotting Parameters & Ice Conditions
- Motion Correction & Defocus in Cryo-EM
- Microscope Alignment & Imaging Limitations
Week 10 Cryo-EM Image Processing, Freezing Techniques
- CTF Estimation & Defocus in Cryo-EM
- Phase Flip & Motion Correction
- High Pressure & Rapid Freezing Methods
- Cryo-Ultra Microtomy & FIB-SEM
- Graphene Oxide Grids in Cryo-EM
Week 11 Cryo-EM Data Processing: Motion Correction to 3D Reconstruction
- Motion Correction & 2D Classification Basics
- Concepts & Methods in 2D/3D Classification
- 3D Reconstruction & Resolution Assessment
Week 12 Hands-on Practical Training in TEM & Cryo-EM
Syllabus and materials
At NPTEL, as the course publishes them.
Credits and licence
- Institution
- IISc Bangalore
- Department
- Biotechnology
- Teacher
- Prof. Somnath Dutta
- Level
- Undergraduate
- Language
- English
- Subjects
- Biology
- Source
- NPTEL
- Licence
- CC BY-NC-SA, as NPTEL states it. Non-commercial use only. NPTEL's terms
- Attribution
- NPTEL states: "Distributed under Creative Commons Attribution-ShareAlike / CC BY - NC - SA", beside a BY-NC-SA badge.
- Who can watch
- NPTEL gives no rating. Invisible Network shows it to Teens profiles and older, judged from what the source says about it. How courses are placed