The Winter-Spring 2020 EM Course

General registration for the 2020 winter course is closed. If you registered for this course through your institution’s registrar (with a cutoff in January), then please let us know as we have separate reserved spots for students taking the course for academic credit.

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), and Peter Shen & Janet Iwasa (CryoEM 101 from University of Utah). 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 or NYSBC seminar rooms (Winter course: Mondays 3:30-5pm and Wednesdays 3:30-5pm | Short course weeks: 9:30am-11am)

EM fundamentals section (month of January)
Jan 6 : Lecture – Introduction & SEMC tour (Ed Eng – NYSBC) – [EE pdf]Jan 8 : Practical – Sample Preparation & Support films (Micah Rapp/Ed Eng – COLU/NYSBC) – [EE pdf]Jan 13 : Lecture – Basic anatomy of the electron microscope (Micah Rapp – COLU) [MR pdf]Jan 15 : Practical – TEM use
Jan 20 : MLK Jr holiday – No class
Jan 22 : Practical – Journal club
Jan 27 : Lecture – Fourier transforms and Image Formation (Micah Rapp – COLU) [MR pdf]Jan 29 : Practical – Image pre-processing
Feb 3 : Lecture – MicroED (Bill Rice – NYU) [WR pdf]Feb 5 : Practical – Journal club
Feb 10: Lecture – Helical reconstruction (Hernando Sosa – Einstein)
Feb 12 : Practical – Journal club
Feb 17 : President’s day holiday – No class
Feb 19 : Practical – Journal club
Feb 24 : Q&A – open forum & primer to SPA
Feb 26 : Practical – Intro to SPA processing

The course handbook may be found here.

Single particle section
March 2 : Short course Keynote – Intro to Single Particle
See SPA short course here. Students that attend the full course will be allowed to participate in the morning lectures, but would have to apply to be admitted to the afternoon practicals.

Tomography section
April 13 : Short course Keynote – Intro to Tomography
See tomography short course here. Students that attend the full course will be allowed to participate in the morning lectures, but would have to apply to be admitted to the afternoon practicals.

Previous courses:

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

  • Part 1: 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.
  • Part 2: 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.

Note: The Zoom links will be emailed to our mailing list. If you have not received the link please check your spam folder or re-register for the course making sure a valid email address is used. If you are taking the course for credit make sure to sign up through your institution’s registrar as well.

  •  CUNY GC course BICM88900, class number 58654 – Special Topics in Biochemistry – 3 credits
  •  Columbia BCHM G6400 – Cryo-Electron Microscopy – 4 credits