The Winter-Spring 2024 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).

Course Schedule

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

EM fundamentals section 
Jan 17: Lecture – Introduction & Basic anatomy of the electron microscope (Ed Eng – NYSBC/SEMC & SEMC staff [pdf])
Jan 22: Lecture – New cryoEM hardware and supporting a facility (Michael Alink – NYSBC/SEMC [pdf])
Jan 24: Practical – TEM use (SEMC staff [worksheet])
Jan 29: Lecture – Considerations for biological cryoEM (Ed Eng – NYSBC/SEMC & SEMC staff [pdf])
Jan 31: Practical – Sample Preparation & Support films (SEMC staff [worksheet])

EM crystallography section
Feb 5: Lecture – MicroED (Bill Rice – New York University [pdf])
Feb 7: Practical – Journal club (On sample vitrification)
Feb 12: Lecture – Helical reconstruction (Hernando Sosa – Albert Einstein College of Medicine [pdf])
Feb 14: Practical – Journal club (On the best keV for biological samples)
Feb 21: Practical – Journal club

Tomography section
Feb 26: Lecture – Tomography (Wei Dai — Rutgers University [pdf])
Feb 28: Practical – Journal Club
Mar 4: Lecture – FIB-SEM (Bill Rice – New York University [pdf])
Mar 6: Lecture  – Tomography software (Alex Noble — NYSBC/SEMC [pdf])

Classes in the NYSBC seminar room (mornings)
Single-particle section* 

Mar 11 : Short course Keynote – Intro to Single Particle
*Mar 11 to Mar 15, 2024 with instructors:

  • Joachim Frank (Columbia University)
  • Victor Chen & Wen Jian (Purdue University)
  • Fred Sigworth (Yale University)
  • Amedee des Georges (New York University) & Reza Khayat (City University of New York)
  • Rich Hite (Memorial Sloan Kettering Cancer Center)
  • Pilar Cossio (Flatiron Institute)
  • Oli Clarke (Columbia University)
  • Gira Bhabha & Damian Ekiert (New York University)

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.

Future perspectives
Mar 18: Lecture – The future of cryoEM (SEMC staff)
Mar 20: Practical – Journal club
Mar 25: Practical – Journal club
Mar 27: Practical – Roundtable (SEMC staff)
Apr 1: Lecture – Wrap up (SEMC staff)

Previous courses:

Materials from previous courses may be found on our left bar.

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
Mahira Aragon (NYSBC): Teaching assistant
Aaron Owji (NYSBC): Teaching assistant
Jessalyn Miller (NYSBC): Teaching assistant
Zephan Melville (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: 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