Getting started in cryo-EM from Coursera

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.

What's inside

Syllabus

Welcome

Welcome to the course!

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

Fourier Transforms and Reciprocal Space for Beginners

Image Formation

Fundamental Challenges in Biological EM

Single Particle Analysis

Tomography

2-D Crystallography

Good to know

Know what's good

, what to watch for

, and possible dealbreakers

Explores the fundamental principles of cryo-electron microscopy and various techniques, which is standard in biological research

Taught by Grant J. Jensen, who is recognized for their work in cryo-electron microscopy

Strengthens an existing foundation for intermediate learners

Develops concepts rather than mathematical details, which is useful for beginners

Provides numerous example images, assisting visualization in understanding complex concepts

Explicitly provides prerequisites, setting clear expectations for the learner's prior knowledge

The preferred pace for going through the modules is not clearly defined, leaving it to the learners to decide

Reviews summary

Cryo-em made easy

Learners say Cryo-EM Made Easy is a wonderful course that teaches the basics of cryo-electron microscopy with engaging lectures that are full of valuable knowledge. According to students, the course is great for beginners and useful for those starting a PhD in Structural Biology. While some students wish there was a certification at the end, most agree that this is one of the best courses they have ever taken.

The lectures in this course are engaging and in-depth.

"Fantastic lectures!"

"Precise, in-depth and full of valuable knowledge."

This course is great for beginners in cryo-EM.

"this is one of the best courses I have ever taken!"

"It is great a course for all the information one need to have on Electron Microscopy from the basic knowledge to Cryo-Electron."

There is no certification for completing the course.

"COURSE COMPLETED CERTIFICATE REQUIRED"

"Very informative. Got to learn a lot. Would be better, if provided as a certification course!"

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in Getting started in cryo-EM with these activities:

Review Basic Principles of Electron Microscopy

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Review the fundamental concepts of electron microscopy to strengthen your foundation for the course.

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Review basic electron microscope anatomy
Revisit the principles of image formation in EM
Explore the challenges associated with biological electron microscopy

Review basic biology and calculus topics

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Reviewing basic biology and calculus concepts will strengthen your foundation for understanding the principles of cryo-EM.

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Review high school biology concepts, such as cell structure and function, genetics, and evolution.
Review calculus concepts, such as derivatives, integrals, and differential equations.

Review Alberts' Molecular Biology of the Cell

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Supplement your understanding of the biological context of cryo-EM by reviewing key concepts in molecular biology from this foundational textbook.

View Molecular Biology of the Cell on Amazon

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Focus on chapters relevant to cell structure and function
Read and take notes on the assigned chapters
Review your notes and identify any areas that require further clarification

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Review Calculus and Linear Algebra

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Strengthen your mathematical foundation by reviewing basic concepts of calculus and linear algebra, which are useful for understanding image processing and data analysis in cryo-EM.

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Review the fundamentals of calculus
Review the basics of linear algebra
Solve practice problems to reinforce your understanding

Review Fourier Transform Fundamentals

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Improves foundational understanding of Fourier Transforms to better prepare for discussions on image formation.

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Read an introductory text on Fourier Transforms.
Go through example problems related to Fourier analysis.

Complete online tutorials on cryo-EM

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Engaging in online tutorials will provide you with hands-on experience and a deeper understanding of cryo-EM techniques.

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Find reputable online tutorials on cryo-EM, such as those offered by universities or research institutions.
Follow the tutorials step-by-step, taking notes and asking questions as needed.

Explore Fourier Transforms and Image Processing Techniques

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Enhance your understanding of Fourier transforms and essential image processing workflows used in cryo-EM.

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Find tutorials on Fourier transforms
Explore tutorials on basic image processing techniques
Apply these techniques to sample cryo-EM images

Create a comprehensive study guide

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Compiling a study guide will help you organize and retain the key concepts covered in the course.

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Review the course syllabus and lecture notes.
Identify important concepts, definitions, and equations.
Create a structured study guide that includes summaries, mind maps, and practice questions.

Image Analysis Exercises

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Reinforce your understanding of image analysis techniques used in cryo-EM by completing hands-on exercises.

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Use software tools to analyze and interpret simulated or real cryo-EM images.
Compare your results with provided solutions or consult with an expert.
Repeat the exercises with different types of images to broaden your experience.

Follow Cryo-EM Image Processing Tutorial

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Enhances practical understanding of cryo-EM image processing techniques through guided instruction.

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Identify and select a comprehensive cryo-EM image processing tutorial.
Follow the tutorial step-by-step, applying the techniques to sample data.
Review and troubleshoot any challenges encountered during the tutorial.

Create a Visual Guide to Cryo-EM Sample Preparation

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Solidify your knowledge of cryo-EM sample preparation by creating a visual guide that outlines the key steps and considerations.

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Research and gather information on cryo-EM sample preparation techniques
Design a flowchart or infographic that visually presents the steps
Include details on sample selection, vitrification, and grid preparation

Create a Summary or Presentation

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Solidify your understanding by creating a summary or presentation that covers key concepts and techniques from the course.

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Identify the main topics and concepts you want to cover.
Gather information from the lectures, readings, and other resources.
Organize and present the information in a clear and concise manner.
Share your summary or presentation with others to receive feedback.

Analyze cryo-EM images

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Practicing image analysis will enhance your ability to interpret and extract meaningful information from cryo-EM data.

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Obtain a set of cryo-EM images from a public database or a research article.
Use image analysis software to process and analyze the images, identifying key features and structures.
Compare your results with published data or consult with an expert for feedback.

Practice Image Analysis for Cryo-EM

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Develops proficiency in image analysis skills crucial for cryo-EM applications.

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Obtain a dataset of cryo-EM images.
Use image analysis software to identify and characterize features within the images.
Compare and contrast different analysis approaches to optimize results.

Participate in a Study Group for Data Collection Strategies

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Engage with peers to discuss and reinforce data collection strategies in cryo-EM, broadening your perspectives.

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Join or form a study group focused on data collection techniques
Prepare by reviewing relevant course materials
Actively participate in discussions and share insights

Follow Online Tutorials on Advanced Topics

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Expand your knowledge and skills by exploring advanced topics through guided online tutorials or workshops.

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Identify specific areas where you want to gain deeper understanding.
Find reputable online tutorials or workshops on these topics.
Follow the tutorials or attend the workshops to learn new techniques and concepts.
Apply what you have learned to your own research or projects.

Create a Model for Understanding Cryo-EM Techniques

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Reinforces understanding of cryo-EM techniques through the process of creating an explanatory model.

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Research and gather information on various cryo-EM techniques.
Develop a visual or interactive model that illustrates the principles and applications of these techniques.
Present or share the model with peers or experts for feedback and refinement.

Practice Image Analysis and Interpretation

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Enhance your image analysis skills by practicing on cryo-EM images, improving your ability to extract meaningful data.

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Obtain a set of cryo-EM images
Use image processing software to analyze and interpret the images
Identify and characterize structural features

Develop a presentation on cryo-EM applications

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Creating a presentation will allow you to synthesize your knowledge of cryo-EM and effectively communicate it to others.

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Research various applications of cryo-EM in different fields, such as structural biology, drug discovery, and materials science.
Organize your findings into a logical and visually appealing presentation.
Practice delivering your presentation to receive constructive feedback.

Develop a Cryo-EM Data Analysis Pipeline

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Apply your knowledge to a practical project by designing and implementing a data analysis pipeline for cryo-EM data, enhancing your problem-solving and technical skills.

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Define the goals and requirements of the pipeline
Choose appropriate software and algorithms
Implement the pipeline and test its functionality

Contribute to open-source cryo-EM software projects

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Contributing to open-source projects will provide you with practical experience and deepen your understanding of cryo-EM software development.

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Identify open-source cryo-EM software projects that align with your interests and skills.
Review the project's documentation and contribute code, bug fixes, or documentation improvements.
Collaborate with other developers to enhance the project's functionality.

Mentor a Student in Cryo-EM

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Deepens understanding of cryo-EM principles and applications through the process of teaching and assisting others.

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Identify a student who is interested in learning about cryo-EM.
Provide guidance and support on cryo-EM concepts and techniques.
Review and discuss cryo-EM-related materials and resources together.

Attend a Workshop on Advanced Cryo-EM Methods

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Provides exposure to cutting-edge cryo-EM methodologies and applications.

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Identify and register for an appropriate workshop.
Attend the workshop and actively participate in discussions and hands-on sessions.
Apply the knowledge and techniques learned to enhance understanding of cryo-EM methods.

Career center

Learners who complete Getting started in cryo-EM will develop knowledge and skills that may be useful to these careers:

Cryo-Electron Microscopy Scientist

A Cryo-Electron Microscopy Scientist is a research scientist who uses cryo-electron microscopy (cryo-EM) to study the structure and function of biological molecules. Cryo-EM is a powerful imaging technique that allows scientists to visualize molecules in their native state, without the need for chemical fixation or staining. This course provides a comprehensive introduction to the principles and applications of cryo-EM, making it an excellent foundation for a career in this field.

See salaries and explore the career path for Cryo-Electron Microscopy Scientist

Structural Biologist

Structural Biologists study the structure and function of biological molecules, such as proteins, nucleic acids, and lipids. They use a variety of techniques to visualize and analyze these molecules, including cryo-electron microscopy (cryo-EM). This course provides a strong foundation in the principles of cryo-EM, making it a valuable resource for Structural Biologists who want to learn more about this powerful technique.

See salaries and explore the career path for Structural Biologist

Molecular Biologist

Molecular Biologists study the structure and function of macromolecules, such as proteins, nucleic acids, and carbohydrates. They use a variety of techniques to study these molecules, including cryo-electron microscopy (cryo-EM). This course provides a comprehensive overview of the principles and applications of cryo-EM, making it a useful resource for Molecular Biologists who want to learn more about this technique.

See salaries and explore the career path for Molecular Biologist

Biophysicist

Biophysicists use the principles of physics to study biological systems. They use a variety of techniques to study these systems, including cryo-electron microscopy (cryo-EM). This course provides a strong foundation in the principles of cryo-EM, making it a valuable resource for Biophysicists who want to learn more about this technique.

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Cell Biologist

Cell Biologists study the structure and function of cells. They use a variety of techniques to visualize and analyze cells, including cryo-electron microscopy (cryo-EM). This course provides a solid introduction to the principles of cryo-EM, making it a helpful resource for Cell Biologists who want to learn more about this technique.

See salaries and explore the career path for Cell Biologist

Research Scientist

Research Scientists conduct scientific research in a variety of fields. They use a variety of techniques to study their research questions, including cryo-electron microscopy (cryo-EM). This course provides a solid introduction to the principles of cryo-EM, making it a helpful resource for Research Scientists who want to learn more about this technique.

See salaries and explore the career path for Research Scientist

Electron Microscopist

Electron Microscopists use electron microscopes to visualize and analyze materials. They use a variety of techniques to prepare samples for microscopy and to analyze images. This course provides a comprehensive overview of the principles and applications of cryo-electron microscopy (cryo-EM), making it a valuable resource for Electron Microscopists who want to learn more about this technique.

See salaries and explore the career path for Electron Microscopist

Microscopy Technician

Microscopy Technicians operate and maintain microscopes. They also prepare samples for microscopy and analyze images. This course provides a comprehensive overview of the principles and applications of cryo-electron microscopy (cryo-EM), making it a valuable resource for Microscopy Technicians who want to learn more about this technique.

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Biomedical Engineer

Biomedical Engineers design and develop medical devices and technologies. They use a variety of techniques to study biological systems, including cryo-electron microscopy (cryo-EM). This course provides a solid introduction to the principles of cryo-EM, making it a helpful resource for Biomedical Engineers who want to learn more about this technique.

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Chemical Engineer

Chemical Engineers design and operate chemical plants and processes. They use a variety of techniques to study chemical reactions and processes, including cryo-electron microscopy (cryo-EM). This course provides a solid introduction to the principles of cryo-EM, making it a helpful resource for Chemical Engineers who want to learn more about this technique.

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Materials Scientist

Materials Scientists study the structure and properties of materials. They use a variety of techniques to study these materials, including cryo-electron microscopy (cryo-EM). This course provides a solid introduction to the principles of cryo-EM, making it a helpful resource for Materials Scientists who want to learn more about this technique.

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Mechanical Engineer

Mechanical Engineers design and build machines and other mechanical devices. They use a variety of techniques to study the behavior of materials and structures, including cryo-electron microscopy (cryo-EM). This course provides a solid introduction to the principles of cryo-EM, making it a helpful resource for Mechanical Engineers who want to learn more about this technique.

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Electrical Engineer

Electrical Engineers design and build electrical systems and devices. They use a variety of techniques to study the behavior of electrical systems, including cryo-electron microscopy (cryo-EM). This course provides a solid introduction to the principles of cryo-EM, making it a helpful resource for Electrical Engineers who want to learn more about this technique.

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Data Scientist

Data Scientists use data to solve problems and make decisions. They use a variety of techniques to analyze data, including cryo-electron microscopy (cryo-EM). This course provides a solid introduction to the principles of cryo-EM, making it a helpful resource for Data Scientists who want to learn more about this technique.

See salaries and explore the career path for Data Scientist

Computer Scientist

Computer Scientists design and build computer systems and software. They use a variety of techniques to study the behavior of computer sistemas, including cryo-electron microscopy (cryo-EM). This course provides a solid introduction to the principles of cryo-EM, making it a helpful resource for Computer Scientists who want to learn more about this technique.

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Getting started in cryo-EM

What's inside

Syllabus

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Reviews summary

Cryo-em made easy

Activities

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