Getting started in cryo-EM

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Opleiderscore: starstarstarstar_halfstar_border 7,2 Coursera (CC) heeft een gemiddelde beoordeling van 7,2 (uit 6 ervaringen)

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Beschrijving

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About this course: 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 …

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When you enroll for courses through Coursera you get to choose for a paid plan or for a free plan

  • Free plan: No certicification and/or audit only. You will have access to all course materials except graded items.
  • Paid plan: Commit to earning a Certificate—it's a trusted, shareable way to showcase your new skills.

About this course: 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.

Created by:  Caltech
  • Taught by:  Grant J. Jensen, Professor of Biophysics and Biology; Investigator, Howard Hughes Medical Institute

    Biology and Biological Engineering
Commitment 14.5 hours of videos Language English How To Pass Pass all graded assignments to complete the course. User Ratings 4.9 stars Average User Rating 4.9See what learners said Coursework

Each course is like an interactive textbook, featuring pre-recorded videos, quizzes and projects.

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Caltech Caltech is a world-renowned science and engineering research and education institution, where extraordinary faculty and students seek answers to complex questions, discover new knowledge, lead innovation, and transform our future. Caltech's mission is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.

Syllabus


WEEK 1


Welcome
Welcome to the course!


3 videos, 3 readings expand


  1. Video: Introduction to the Course
  2. Reading: Welcome from Professor Jensen
  3. Reading: About the Instructor
  4. Video: Description of Parts
  5. Video: Introduction: Why Electrons?
  6. Reading: Concept Check Questions: Why Electrons?


WEEK 2


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



9 videos, 8 readings expand


  1. Video: Introduction: Basic Anatomy of the EM
  2. Video: Electron Guns
  3. Reading: Concept Check Questions: Electron Guns
  4. Video: EM Lenses
  5. Reading: Concept Check Questions: Electron Lenses
  6. Video: The Column
  7. Reading: Concept Check Questions: The Column
  8. Video: Sample Chamber
  9. Reading: Concept Check Questions: The Sample Chamber
  10. Video: Energy Filters
  11. Reading: Concept Check Questions: Energy Filters
  12. Video: Detectors
  13. Reading: Concept Check Questions: Electron Detectors
  14. Video: Vacuum Systems
  15. Reading: Concept Check Questions: Vacuum Systems
  16. Video: Summary and Safety
  17. Reading: Concept Check Questions: Summary and Safety


WEEK 3


Fourier Transforms and Reciprocal Space for Beginners



7 videos, 6 readings expand


  1. Video: Introduction: Fourier Transforms for Beginnners
  2. Video: 1-D Sine Waves and their Sums
  3. Reading: Concept Check Questions: 1-D Sine Waves and Their Sums
  4. Video: 1-D Reciprocal Space
  5. Reading: Concept Check Questions: 1-D Reciprocal Space
  6. Video: 2-D Waves and Images
  7. Reading: Concept Check Questions: 2-D Waves and Images
  8. Video: 2-D Transforms and Filters
  9. Reading: Concept Check Questions: 2-D Transforms and Filters
  10. Video: 3-D Waves and Transforms
  11. Reading: Concept Check Questions: 3-D Waves and Transforms
  12. Video: Convolution and Cross-Correlation
  13. Reading: Concept Check Questions: Convolution and Cross-correlation


WEEK 4


Image Formation



7 videos, 6 readings expand


  1. Video: Introduction: Image Formation
  2. Video: Amplitude and Phase Contrast
  3. Reading: Concept Check Questions: Amplitude and Phase Contrast
  4. Video: Wave Propagation and Phase Shifts
  5. Reading: Concept Check Questions: Wave Propagation and Phase Shifts
  6. Video: The Contrast Transfer Function
  7. Reading: Concept Check Questions: The Contrast Transfer Function
  8. Video: Defocus and its Effects
  9. Reading: Concept Check Questions: Defocus and its Effects
  10. Video: Envelopes
  11. Reading: Concept Check Questions: Envelopes
  12. Video: CTF Correction
  13. Reading: Concept Check Questions: CTF Correction


WEEK 5


Fundamental Challenges in Biological EM



6 videos, 5 readings expand


  1. Video: Introduction: Fundamental Challenges in Biological EM
  2. Video: Sample Prep - Room Temperature Methods
  3. Reading: Concept Check Questions: Sample Prep - Room Temperature Methods
  4. Video: Sample Prep Methods Involving Freezing
  5. Reading: Concept Check Questions: Sample Prep - Methods Involving Freezing
  6. Video: Sample Prep Grids
  7. Reading: Concept Check Questions: Sample Prep - Grids
  8. Video: 3-D Reconstruction
  9. Reading: Concept Check Questions: 3-D Reconstruction
  10. Video: Dose Limitations
  11. Reading: Concept Check Questions: Dose Limitations


WEEK 6


Single Particle Analysis



5 videos, 6 readings expand


  1. Reading: Concept check questions: Introduction to single particle analysis
  2. Video: Special sample prep issues
  3. Reading: Concept Check Questions: Special sample prep issues
  4. Video: Data collection (imaging)
  5. Reading: Concept Check Questions: Data collection (imaging)
  6. Video: Reconstruction basics
  7. Reading: Concept Check Questions: Reconstruction basics
  8. Video: Reconstruction: additional topics
  9. Reading: Concept Check Questions: Reconstruction - additional topics
  10. Video: Interpretation and limitations
  11. Reading: Concept Check Questions: Interpretation and limitations


WEEK 7


Tomography



5 videos, 5 readings expand


  1. Video: Introduction: Tomography
  2. Reading: Concept Check Questions: Introduction: Tomography
  3. Video: Tomography Data Collection and Reconstruction
  4. Reading: Concept Check Questions: Tomography Data Collection and Reconstruction
  5. Video: Tomography Identifying Objects of Interest
  6. Reading: Concept Check Questions: Identifying Objects in Tomograms
  7. Video: Tomography Limitations
  8. Reading: Concept Check Questions: Tomography Limitations
  9. Video: Tomography Parameters and Handedness
  10. Reading: Concept Check Questions: Tomography Parameters and Handedness


WEEK 8


2-D Crystallography



5 videos, 4 readings expand


  1. Video: Introduction: 2-D Crystallography and Sample Prep
  2. Reading: Concept Check Questions: Introduction: 2-D Crystallography and Sample Prep
  3. Video: FT of a 2-D Crystal
  4. Reading: Concept Check Questions: Fourier Transform of a 2-D Crystal
  5. Video: 2-D Crystallography Data Collection and Reconstruction
  6. Reading: Concept Check Questions: Data Collection and Reconstruction
  7. Video: Helical Tubes
  8. Video: Farewell
  9. Reading: Concept Check Questions: Helical Tubes

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