Caltech - Getting started in cryo-EM
- Offered byCoursera
Getting started in cryo-EM at Coursera Overview
Duration | 21 hours |
Start from | Start Now |
Total fee | Free |
Mode of learning | Online |
Schedule type | Self paced |
Official Website | Explore Free Course  |
Credential | Certificate |
Getting started in cryo-EM at Coursera Highlights
- 100% online Start instantly and learn at your own schedule.
- Flexible deadlines Reset deadlines in accordance to your schedule.
- Approx. 21 hours to complete
- English Subtitles: French, Portuguese (European), Russian, English, Spanish
Getting started in cryo-EM at Coursera Course details
- This class covers the fundamental principles underlying cryo-electron microscopy (cryo-EM) starting with the basic anatomy of electron microscopes, an introduction to Fourier transforms, and the principles of image formation. Building upon that foundation, the class then covers the sample preparation issues, data collection strategies, and basic image processing workflows for all 3 basic modalities of modern cryo-EM: tomography, single particle analysis, and 2-D crystallography.
- Philosophy:
- The course emphasizes concepts rather than mathematical details, taught through numerous drawings and example images. It is meant for anyone interested in the burgeoning fields of cryo-EM and 3-D EM, including cell biologists or molecular biologists without extensive training in mathematics or imaging physics and practicing electron microscopists who want to broaden their understanding of the field. The class is perfect as a primer for anyone who is about to be trained as a cryo-electron microscopist, or for anyone who needs an introduction to the field to be able to understand the literature or the talks and conversations they will hear at cryo-EM meetings.
- Pre-requisites:
- The recommended prerequisites are college-freshman-level math, physics, and biochemistry.
- Pace:
- There are 14.5 hours of lecture videos total separated into 40 individual ?modules? lasting on average 20 minutes each. Each module has at the end a list of ?concept check? questions you can use to test your knowledge of what was presented. As the modules are grouped into seven major subjects, one reasonable plan would be to go through one major subject each day. That would mean watching a couple hours of lecture and spending another hour or so thinking through the concept check questions each day for a week. Another reasonable plan would be to go through one module each day for a little over a month, or even three modules a week (Monday, Wednesday, and Friday) for a 3-month term.
- It is likely that as you then move on to actually begin using a cryo-EM or otherwise engage in the field, you will want to repeat certain modules.
Getting started in cryo-EM at Coursera Curriculum
Welcome
Introduction to the Course
Description of Parts
Introduction: Why Electrons?
Welcome from Professor Jensen
About the Instructor
Concept Check Questions: Why Electrons?
Currents, Coils, Knobs and Names: Basic anatomy of the electron microscope
Introduction: Basic Anatomy of the EM
Electron Guns
EM Lenses
The Column
Sample Chamber
Energy Filters
Detectors
Vacuum Systems
Summary and Safety
Concept Check Questions: Electron Guns
Concept Check Questions: Electron Lenses
Concept Check Questions: The Column
Concept Check Questions: The Sample Chamber
Concept Check Questions: Energy Filters
Concept Check Questions: Electron Detectors
Concept Check Questions: Vacuum Systems
Concept Check Questions: Summary and Safety
Fourier Transforms and Reciprocal Space for Beginners
Introduction: Fourier Transforms for Beginnners
1-D Sine Waves and their Sums
1-D Reciprocal Space
2-D Waves and Images
2-D Transforms and Filters
3-D Waves and Transforms
Convolution and Cross-Correlation
Concept Check Questions: 1-D Sine Waves and Their Sums
Concept Check Questions: 1-D Reciprocal Space
Concept Check Questions: 2-D Waves and Images
Concept Check Questions: 2-D Transforms and Filters
Concept Check Questions: 3-D Waves and Transforms
Concept Check Questions: Convolution and Cross-correlation
Image Formation
Introduction: Image Formation
Amplitude and Phase Contrast
Wave Propagation and Phase Shifts
The Contrast Transfer Function
Defocus and its Effects
Envelopes
CTF Correction
Concept Check Questions: Amplitude and Phase Contrast
Concept Check Questions: Wave Propagation and Phase Shifts
Concept Check Questions: The Contrast Transfer Function
Concept Check Questions: Defocus and its Effects
Concept Check Questions: Envelopes
Concept Check Questions: CTF Correction
Fundamental Challenges in Biological EM
Introduction: Fundamental Challenges in Biological EM
Sample Prep - Room Temperature Methods
Sample Prep Methods Involving Freezing
Sample Prep Grids
3-D Reconstruction
Dose Limitations
Concept Check Questions: Sample Prep - Room Temperature Methods
Concept Check Questions: Sample Prep - Methods Involving Freezing
Concept Check Questions: Sample Prep - Grids
Concept Check Questions: 3-D Reconstruction
Concept Check Questions: Dose Limitations
Single Particle Analysis
Special sample prep issues
Data collection (imaging)
Reconstruction basics
Reconstruction: additional topics
Interpretation and limitations
Concept check questions: Introduction to single particle analysis
Concept Check Questions: Special sample prep issues
Concept Check Questions: Data collection (imaging)
Concept Check Questions: Reconstruction basics
Concept Check Questions: Reconstruction - additional topics
Concept Check Questions: Interpretation and limitations
Tomography
Introduction: Tomography
Tomography Data Collection and Reconstruction
Tomography Identifying Objects of Interest
Tomography Limitations
Tomography Parameters and Handedness
Concept Check Questions: Introduction: Tomography
Concept Check Questions: Tomography Data Collection and Reconstruction
Concept Check Questions: Identifying Objects in Tomograms
Concept Check Questions: Tomography Limitations
Concept Check Questions: Tomography Parameters and Handedness
2-D Crystallography
Introduction: 2-D Crystallography and Sample Prep
FT of a 2-D Crystal
2-D Crystallography Data Collection and Reconstruction
Helical Tubes
Farewell
Concept Check Questions: Introduction: 2-D Crystallography and Sample Prep
Concept Check Questions: Fourier Transform of a 2-D Crystal
Concept Check Questions: Data Collection and Reconstruction
Concept Check Questions: Helical Tubes
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