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Getting started in cryo-EM
  • Level Foundation
  • Duration 21 hours
  • Course by Caltech
  • Offered by

About

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.

Modules

Welcome

    • 3 Videos
    • 3 Readings
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3 Videos

  • Introduction to the Course
  • Description of Parts
  • Introduction: Why Electrons?

3 Readings

  • Welcome from Professor Jensen
  • About the Instructor
  • Concept Check Questions: Why Electrons?

Currents, Coils, Knobs and Names: Basic anatomy of the electron microscope

    • 9 Videos
    • 8 Readings
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9 Videos

  • Introduction: Basic Anatomy of the EM
  • Electron Guns
  • EM Lenses
  • The Column
  • Sample Chamber
  • Energy Filters
  • Detectors
  • Vacuum Systems
  • Summary and Safety

8 Readings

  • 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

    • 7 Videos
    • 6 Readings
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7 Videos

  • 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

6 Readings

  • 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

    • 7 Videos
    • 6 Readings
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7 Videos

  • Introduction: Image Formation
  • Amplitude and Phase Contrast
  • Wave Propagation and Phase Shifts
  • The Contrast Transfer Function
  • Defocus and its Effects
  • Envelopes
  • CTF Correction

6 Readings

  • 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

    • 6 Videos
    • 5 Readings
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6 Videos

  • Introduction: Fundamental Challenges in Biological EM
  • Sample Prep - Room Temperature Methods
  • Sample Prep Methods Involving Freezing
  • Sample Prep Grids
  • 3-D Reconstruction
  • Dose Limitations

5 Readings

  • 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

Introduction to single particle analysis

    • 5 Videos
    • 6 Readings
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5 Videos

  • Special sample prep issues
  • Data collection (imaging)
  • Reconstruction basics
  • Reconstruction: additional topics
  • Interpretation and limitations

6 Readings

  • 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

    • 5 Videos
    • 5 Readings
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5 Videos

  • Introduction: Tomography
  • Tomography Data Collection and Reconstruction
  • Tomography Identifying Objects of Interest
  • Tomography Limitations
  • Tomography Parameters and Handedness

5 Readings

  • 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

    • 5 Videos
    • 4 Readings
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5 Videos

  • Introduction: 2-D Crystallography and Sample Prep
  • FT of a 2-D Crystal
  • 2-D Crystallography Data Collection and Reconstruction
  • Helical Tubes
  • Farewell

4 Readings

  • 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

Auto Summary

"Getting Started in Cryo-EM" is an engaging foundational course designed for those looking to delve into the world of cryo-electron microscopy (cryo-EM). Offered in the Science & Engineering domain, this course is taught by Coursera and spans 14.5 hours of comprehensive lecture videos, divided into 40 easily digestible modules. Each module averages 20 minutes and concludes with concept check questions to reinforce learning. The course begins with the basic anatomy of electron microscopes, introduces Fourier transforms, and explains the principles of image formation. It then guides learners through sample preparation, data collection strategies, and basic image processing workflows across three key cryo-EM modalities: tomography, single particle analysis, and 2-D crystallography. Emphasizing conceptual understanding over mathematical complexity, the course is rich with drawings and example images to aid comprehension. Ideal for cell and molecular biologists without extensive math or imaging physics backgrounds, as well as practicing electron microscopists seeking to expand their knowledge, this course is a perfect primer for future cryo-electron microscopists. It also serves those who need a solid introduction to the field for better engagement with cryo-EM literature and discussions. With a flexible pace, learners can choose to complete the course over a week, a month, or even spread it out over a three-month term, allowing for a tailored learning experience. The course is accessible via Coursera's Starter or Professional subscription plans, making it a valuable resource for anyone eager to understand the burgeoning field of cryo-EM. Prerequisites include basic college-level math, physics, and biochemistry.

Grant J. Jensen
Instructor

Grant J. Jensen