The Winter-Spring 2022 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.

The course will be held at the New York Structural Biology Center at 89 Convent Ave (133rd St).

Course Schedule

Classes in SEMC seminar room (Mondays 3:30-5pm and select Wednesdays 3:30-5pm)

EM fundamentals section (month of January)

Lecture1 : Introduction & SEMC tour 
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 in the SEMC conference room (starts @3:30pm)

Course instructors:

Edward Eng (NYSBC, Manager): Course leader

Micah Rapp (COLU, Graduate student): Teaching assistant


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

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

Suggested class structure (1.5 hr class)

  • Introduction by guest lecturer on applying the class topic to scientific questions with focus on the nuts & bolts of the technique. Examples may be from their own research or recent papers.
  • Open ended discussion on the topic. Conversation starters may come from concept check questions on the topic or presentation on newer developments in the field.


2020-08-24T20:25:22+00:00August 24th, 2020|Courses|