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. Each week guest lecturers and SEMC staff lead discussions on the practice of solving molecular structures by electron microscopy. Students will be responsible for watching relevant sections from Getting Started in Cryo-EM and cryoEM101 ahead of attending the lectures.

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

Course Schedule

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

EM fundamentals section 
1/10/22 Lecture – Introduction & Basic anatomy of the electron microscope (Ed Eng, SEMC/NYSBC) [pdf] 1/12/22 Practical – TEM use (SEMC staff) [pdf].
1/17/22 MLK Jr holiday – No class
1/19/22 Practical – Sample Preparation & Support films (SEMC staff) [pdf][livestream].
1/24/22 Lecture – New cryoEM hardware and supporting a facility (Michael Alink, SEMC/NYSBC) [pdf][livestream].
1/26/22 Practical – Journal club – Sample vitrification [paper1][paper2][livestream].

EM crystallography section
1/31/22 Lecture – MicroED (Bill Rice – New York University) [pdf][livestream].
2/2/22 Practical – Journal club – Microscope voltage [paper1][paper2][livestream].
2/7/22 Lecture – Helical reconstruction (Hernando Sosa – Einstein) [pdf][livestream].
2/9/22 Practical – Processing practical (SEMC staff) [cryoSPARC tutorial].

Tomography section
2/14/22 Lecture – Tomography (Wei Dai — Rutgers University) [pdf][livestream].
2/16/22 Practical – Journal Club – Resolution revolution [paper1][paper2][livestream].
2/21/22 President’s day holiday – No class
2/23/22 Practical – Journal club – HIV trimer controversy [paper1][paper2][paper3][response].
2/28/22 Lecture – FIB-SEM (Bill Rice – New York University) [pdf][livestream].
3/2/22 Lecture & Practical – Tomography workshop – Appion/Protomo (Alex Noble — NYSBC/SEMC) [pdf].
3/7/22 Practical – Journal club – EM validation [paper1][paper2].
3/9/22 Practical – Journal club – Time resolved EM [paper1][paper2]

Classes in the NYSBC seminar room (mornings)

Single-particle section* 
3/14/22 : Short course Keynote – Intro to Single Particle
*3/14-18/22 with instructors:

Joachim Frank (Columbia University) [pdf] Victor Chen & Wen Jian (Purdue University) [pdf] Fred Sigworth (Yale University) [pdf1 pdf2] Amedee des Georges & Reza Khayat (ASRC/City University of New York) [pdf] Rich Hite (Memorial Sloan Kettering Cancer Center) [pdf] Tom Walz (Rockefeller University) [pdf] Cathy Lawson (Rutgers University) [pdf] Oli Clarke (Columbia University) [pdf] Gira Bhabha & Damian Ekiert (New York University) [pdf]

The single particle section will be a 1-week short course. See more information on the 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.

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, the 2020 course may be found here and 2021 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
Christina Zimanyi (NYSBC): Lead Teaching assistant
Mahira Aragon (NYSBC): Teaching assistant
Eugene Chua (NYSBC): 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