The Winter-Spring 2023 EM Course

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 based on Grant Jensen’s online course (Getting Started in Cryo-EM from Caltech). Students will be responsible for watching these online lectures prior to class. Each week guest lecturers and SEMC staff lead discussions 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 . Classes will be held Mondays 3:30-5pm and select Wednesdays 3:30-5pm. Times may be subject to change.


Class topics

EM fundamentals section 

Lecture1 : Introduction Lecture2 : Basic anatomy of the electron microscope Lecture3 : Challenges in biological EM & Sample Prep and practical Lecture4 : Support films and practical Lecture5: Fourier transforms and Image Formation

Tomography section

Lecture1: Tomography (part I: Intro and overview of ET) Lecture2 : Tomography (part II: FIB-SEM) Lecture3 : Tomography (part III: Cryo-Applications & Sub-tomogram averaging)

Single particle section

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

EM crystallography section

Lecture1 : MicroED and 2D crystallography intro Lecture2 : Helical (part I: Intro and overview of helical) Lecture3 : Helical (part II: Helical cont)

EM challenges and new frontiers

Lecture1 : Validation methods Lecture2 : EMDataBank: Structure Data Archiving, Validation Challenges Lecture3 : Moderate resolution interpretation Lecture4 : Fitting Atomic Models


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)
2020-09-08T21:49:45+00:00September 8th, 2020|Courses|