Throughout the course, students will learn about the different types of electron microscopes and the principles of cryo-EM sample preparation and imaging. They will also explore the different steps involved in cryo-EM image processing and 3D reconstruction of macromolecular structures.
The course covers various topics related to cryo-EM, including image formation, resolution, and validation. Students will also learn about the latest advances in cryo-EM technology and its impact on the field of structural biology.
The course consists of several modules, with each module containing video lectures, quizzes, and exercises to reinforce learning. Students can also participate in discussion forums to connect with other learners and ask questions.
By the end of the course, students will have gained a basic understanding of cryo-EM and its applications in structural biology. They will also have learned how to critically evaluate cryo-EM data and communicate effectively about cryo-EM-related topics. Overall, the course is ideal for anyone interested in a career in structural biology or biophysics.
The Getting started in cryo-EM course by Grant J. Jensen on Coursera consists of 8 modules, detailed as follows:
Module 1: Welcome (3 videos + 3 readings)
Welcome to the course!
3 videosTotal 19 minutes
- Introduction to the CoursePreview module 2 minutes
- Description of Parts 7 minutes
- Introduction: Why Electrons? 8 minutes
3 readingsTotal 30 minutes
- Welcome from Professor Jensen 10 minutes
- About the Instructor 10 minutes
- Concept Check Questions: Why Electrons? 10 minutes
Module 2: Currents, Coils, Knobs and Names: Basic anatomy of the electron microscope (9 videos + 8 readings)
9 videosTotal 93 minutes
- Introduction: Basic Anatomy of the EMPreview module 0 minutes
- Electron Guns 18 minutes
- EM Lenses 0 minutes
- The Column 26 minutes
- Sample Chamber 14 minutes
- Energy Filters 7 minutes
- Detectors 11 minutes
- Vacuum Systems 9 minutes
- Summary and Safety 5 minutes
8 readingsTotal 80 minutes
- Concept Check Questions: Electron Guns 10 minutes
- Concept Check Questions: Electron Lenses 10 minutes
- Concept Check Questions: The Column 10 minutes
- Concept Check Questions: The Sample Chamber 10 minutes
- Concept Check Questions: Energy Filters 10 minutes
- Concept Check Questions: Electron Detectors 10 minutes
- Concept Check Questions: Vacuum Systems 10 minutes
- Concept Check Questions: Summary and Safety 10 minutes
Module 3: Fourier Transforms and Reciprocal Space for Beginners (7 videos + 6 readings)
7 videosTotal 134 minutes
- Introduction: Fourier Transforms for BeginnnersPreview module 0 minutes
- 1-D Sine Waves and their Sums 32 minutes
- 1-D Reciprocal Space 20 minutes
- 2-D Waves and Images 19 minutes
- 2-D Transforms and Filters 32 minutes
- 3-D Waves and Transforms 13 minutes
- Convolution and Cross-Correlation 15 minutes
6 readingsTotal 60 minutes
- Concept Check Questions: 1-D Sine Waves and Their Sums 10 minutes
- Concept Check Questions: 1-D Reciprocal Space 10 minutes
- Concept Check Questions: 2-D Waves and Images 10 minutes
- Concept Check Questions: 2-D Transforms and Filters 10 minutes
- Concept Check Questions: 3-D Waves and Transforms 10 minutes
- Concept Check Questions: Convolution and Cross-correlation 10 minutes
Module 4: Image Formation (7 videos + 6 readings)
7 videosTotal 164 minutes
- Introduction: Image FormationPreview module 0 minutes
- Amplitude and Phase Contrast 30 minutes
- Wave Propagation and Phase Shifts 30 minutes
- The Contrast Transfer Function 33 minutes
- Defocus and its Effects 21 minutes
- Envelopes 16 minutes
- CTF Correction 31 minutes
6 readingsTotal 60 minutes
- Concept Check Questions: Amplitude and Phase Contrast 10 minutes
- Concept Check Questions: Wave Propagation and Phase Shifts 10 minutes
- Concept Check Questions: The Contrast Transfer Function 10 minutes
- Concept Check Questions: Defocus and its Effects 10 minutes
- Concept Check Questions: Envelopes 10 minutes
- Concept Check Questions: CTF Correction 10 minutes
Module 5: Fundamental Challenges in Biological EM (6 videos + 5 readings)
6 videosTotal 95 minutes
- Introduction: Fundamental Challenges in Biological EMPreview module 3 minutes
- Sample Prep - Room Temperature Methods 20 minutes
- Sample Prep Methods Involving Freezing 27 minutes
- Sample Prep Grids 11 minutes
- 3-D Reconstruction 11 minutes
- Dose Limitations 22 minutes
5 readingsTotal 50 minutes
- Concept Check Questions: Sample Prep - Room Temperature Methods 10 minutes
- Concept Check Questions: Sample Prep - Methods Involving Freezing 10 minutes
- Concept Check Questions: Sample Prep - Grids 10 minutes
- Concept Check Questions: 3-D Reconstruction 10 minutes
- Concept Check Questions: Dose Limitations 10 minutes
Module 6: Single Particle Analysis (5 videos + 6 readings)
5 videosTotal 158 minutes
- Special sample prep issuesPreview module 22 minutes
- Data collection (imaging) 21 minutes
- Reconstruction basics 31 minutes
- Reconstruction: additional topics 44 minutes
- Interpretation and limitations 38 minutes
6 readingsTotal 60 minutes
- Concept check questions: Introduction to single particle analysis 10 minutes
- Concept Check Questions: Special sample prep issues 10 minutes
- Concept Check Questions: Data collection (imaging) 10 minutes
- Concept Check Questions: Reconstruction basics 10 minutes
- Concept Check Questions: Reconstruction - additional topics 10 minutes
- Concept Check Questions: Interpretation and limitations 10 minutes
Module 7: Tomography (5 videos + 5 readings)
5 videosTotal 130 minutes
- Introduction: TomographyPreview module 23 minutes
- Tomography Data Collection and Reconstruction 40 minutes
- Tomography Identifying Objects of Interest 24 minutes
- Tomography Limitations 29 minutes
- Tomography Parameters and Handedness 12 minutes
5 readingsTotal 50 minutes
- Concept Check Questions: Introduction: Tomography 10 minutes
- Concept Check Questions: Tomography Data Collection and Reconstruction 10 minutes
- Concept Check Questions: Identifying Objects in Tomograms 10 minutes
- Concept Check Questions: Tomography Limitations 10 minutes
- Concept Check Questions: Tomography Parameters and Handedness 10 minutes
Module 8: 2-D Crystallography (5 videos + 4 readings)
5 videosTotal 54 minutes
- Introduction: 2-D Crystallography and Sample PrepPreview module 6 minutes
- FT of a 2-D Crystal 24 minutes
- 2-D Crystallography Data Collection and Reconstruction 17 minutes
- Helical Tubes 3 minutes
- Farewell 2 minutes
4 readingsTotal 40 minutes
- Concept Check Questions: Introduction: 2-D Crystallography and Sample Prep 10 minutes
- Concept Check Questions: Fourier Transform of a 2-D Crystal 10 minutes
- Concept Check Questions: Data Collection and Reconstruction 10 minutes
- Concept Check Questions: Helical Tubes 10 minutes
As a student who has taken the Getting started in cryo-EM course by Grant J. Jensen on Coursera, I can say that the course is an outstanding introduction to the field of cryo-electron microscopy. The course covers a wide range of topics, from sample preparation and imaging to data analysis and interpretation, and it does so in a way that is clear, concise, and easy to follow.
One of the things I appreciated most about the course was the way in which it combined theoretical concepts with practical applications. The course provides a solid foundation in the fundamental principles of cryo-EM, but it also goes into great detail on the practical aspects of the technique, such as how to optimize sample preparation and how to use the EMAN2 software package to process and analyze data. This combination of theory and practice is essential for anyone who wants to use cryo-EM in their research, and the course does an excellent job of providing both.
Another strength of the course is the way in which it is structured. The course is divided into 8 modules, each of which covers a specific aspect of cryo-EM. Within each module, there are several lectures, as well as quizzes and assignments that help students to assess their understanding of the material. The quizzes and assignments are challenging but manageable, and they provide valuable opportunities for students to reinforce their knowledge and receive feedback on their progress.
One minor criticism I have of the course is that it does assume some prior knowledge of biology and chemistry. While the course does provide some introductory lectures on these topics, students who are completely new to these subjects may find some of the material challenging. However, this is a minor quibble, and overall, the course does an excellent job of balancing accessibility with rigor.
Overall, I would highly recommend the Getting started in cryo-EM course to anyone who is interested in learning about this exciting and rapidly advancing field. The course is engaging, informative, and practical, and it provides a solid foundation for anyone who wants to use cryo-EM in their research.
At the time, the course has an average rating of 4.9 out of 5 stars based on over 267 ratings.
What you'll learn:
Upon completion of the Getting started in cryo-EM course by Grant J. Jensen on Coursera, students will have acquired the following skills:
- Understanding of the fundamental principles of cryo-EM and how to apply it to study complex protein structures and other biological systems.
- Ability to select and prepare samples for cryo-EM, including techniques such as sample purification, protein isolation, sample packaging, and especially cryo-EM grid preparation to generate the best sample preparations for cryo-EM.
- Mastery of the equipment and technologies used in cryo-EM, especially electron microscopy and related image processing software.
- Ability to process data and reconstruct 3D biological structures from cryo-EM data, including techniques such as particle picking, image processing, 3D reconstruction, refinement, and validation.
- Ability to understand and interpret research results from cryo-EM data and present them in a scientific and clear manner.
In summary, after completing this course, students will have gained a strong foundation in cryo-EM and the necessary skills to participate in research projects in this field. The course covers a range of topics from sample preparation to data analysis and interpretation, providing a comprehensive understanding of the cryo-EM process. Students will also have opportunities to work with real data and learn from experts in the field, further enhancing their skills and knowledge.
Grant J. Jensen is a distinguished Professor of Biomedical Engineering and Biological Sciences at the California Institute of Technology (Caltech). He received his Ph.D. from the University of California, Los Angeles (UCLA) and completed his postdoctoral research at the University of Oxford in the UK.
Jensen is a leading expert in the field of cryo-electron microscopy (cryo-EM), a powerful technique used to determine the three-dimensional structures of biological macromolecules. He has made significant contributions to the development of cryo-EM methodologies and has applied these techniques to study a wide range of biological systems, including viruses, bacterial cells, and eukaryotic cells.
In addition to his research contributions, Jensen is a dedicated educator and has taught courses in cryo-EM and structural biology at Caltech and through online platforms such as Coursera. He is also a member of numerous scientific organizations and has received several awards for his research accomplishments, including the National Institutes of Health (NIH) Director's Pioneer Award and the American Society for Cell Biology (ASCB) Prize for Excellence in Inclusivity.
Overall, Grant J. Jensen is a highly respected and accomplished scientist in the field of cryo-EM. His contributions to the development and application of cryo-EM have greatly advanced the field and his dedication to education has helped to train the next generation of cryo-EM researchers.
The requirements for the Getting started in cryo-EM course by Grant J. Jensen on Coursera are as follows:
Basic knowledge of biology and chemistry: Students should have a basic understanding of fundamental concepts in biology and chemistry, including molecules, cells, and proteins. This will enable them to understand the principles of cryo-EM, which relies on the imaging of biological macromolecules.
Basic computer skills: Students should be familiar with basic computer skills such as navigating a file system, using a web browser, and installing software. This will allow them to download and install the required software for the course, and to access the course materials and resources.
Access to required software: Students must have access to the EMAN2 software package, which is used for image processing in the course. This software can be downloaded for free from the EMAN2 website, and students should ensure that their computer meets the software's system requirements.
Access to appropriate hardware: Students must have access to a computer with sufficient processing power and memory to run the required software. The recommended specifications for the computer are a multi-core processor with a clock speed of 2.4 GHz or higher, at least 16 GB of RAM, and a dedicated graphics card with at least 4 GB of VRAM.
Access to a cryo-EM facility: While not required, access to a cryo-EM facility is recommended to gain hands-on experience in sample preparation and imaging. If a student does not have access to a cryo-EM facility, they can still complete the course but may not have practical experience with the technique.
English language proficiency: The course is conducted in English, so students should have a sufficient level of English proficiency to understand lectures, read materials, and participate in discussions. Students who are not fluent in English may struggle to understand the course content and participate fully in the course.
Overall, the course requirements ensure that students have the necessary technical resources and background knowledge to participate fully in the course and gain a comprehensive understanding of cryo-EM.