The Winter-Spring 2021 EM Course

Due to the COVID-19 health situation this will be a remote class.

Sign up for this course by pre-registering here: . Students taking this course for credit should also register with their institution’s registrar.

About the course

Electron microscopy in combination with image analysis is increasingly powerful in producing 3D structures of individual molecules and large macromolecular complexes that are unapproachable by other methods. This course is focused on the concepts and theories behind electron microscopy and will be taught in a reverse classroom format with pre-recorded lectures. Students will be responsible for watching these online lectures prior to class, which will be live roundtable discussions led by guest lecturers and SEMC staff on the practice of solving molecular structures by electron microscopy.


Class structure (1.5 hr class)

The course will be offered by the New York Structural Biology Center but given the COVID-19 health situation will be held virtually. Classes will be held by Zoom (Mondays 3:30-5pm and select Wednesdays 3:30-5pm). Times may be subject to change. 

  • Pre-recorded lectures and other online content from previous years will be used.
  • Weekly roundtable discussions to supplement the online content. Open-ended discussions on the topic will be lead by course instructors after a brief introduction to the topic. Conversation starters may come from concept check questions from Grant Jensen’s online course (Getting Started in Cryo-EM from Caltech) or presentation on newer developments in the field.
  • The weekly meetings will be supplemented by Journal Clubs and remote practicals.


Class topics

EM fundamentals section (month of January)

Lecture1 : Jan 11 – Introduction & Basic anatomy of the electron microscope
Lecture2 : Jan 13 – Challenges in biological EM & Sample Prep and practical
Lecture3 : Jan 20 – Support films and practical
Lecture4: Jan 25 – Fourier transforms and Image Formation

EM crystallography section

Lecture1 : Feb 1 – MicroED and 2D crystallography intro 
Lecture2 : Feb 8 – Helical (Intro and overview of helical) 

Single particle section

Lecture1: Feb 22 – Single-particle analysis (part I: Intro and overview of SPA) 
Lecture2 : Mar 1 – Single-particle analysis (part II: Data Analysis and reconstruction workflow 
Lecture3 : Mar 8 – Single-particle analysis (part III: Reconstruction workflow (cont), and Interpretation and Limitations)

EM challenges and new frontiers

Lecture1 : Mar 15 – Validation methods 
Lecture2 : Mar 17 – EMDataBank: Structure Data Archiving, Validation Challenges 
Lecture3 : Mar 22 – Model refinement and validation
Lecture4 : Mar 29 – Tips and tricks for manual model building of atomic models into cyryoEM maps

Tomography section

1 week in April covering:

  • Intro and overview of ET
  • CryoCLEM-FIB-ET workflow
  • Cryo-Applications and sub-tomogram averaging
  • Choosing the right in situ target and model system
  • Automated reconstruction, subtomogram averaging methods & data interpretation
  • EMAN2 tools, sub-tomogram averaging and annotation
  • The future of in situ cellular structural biology


Previous courses:

Lecture slides from the 2016 course may be found here, 2017 course may be found here, 2018 course may be found here, 2019 course may be found here and the 2020 course may be found here.

The lecture slides are provided for educational purposes only. All rights are reserved by their original authors. Please contact them if you would like to use or repost their content.



Practicals/Journal club will be regularly scheduled over the semester to supplement the instruction. Typically on Wednesday @3:30pm.



For researchers taking the course for credit, the final score will be tabulated as follows:

  • Recitation 40%
  • Practical Worksheet 10% x 4
  • Attendance 20%



  • Course coordinator: Ed Eng (NYSBC)
  • Teaching assistant: Micah Rapp (Columbia/NYSBC)



2020-09-09T01:58:16+00:00October 16th, 2019|Courses|