The Winter-Spring 2019 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) or Zoom (when appropriate).

Course Schedule

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

EM fundamentals section (month of January)
Jan 7 : Introduction & SEMC tour [Ed Eng, NYSBC] [pdf EE] Jan 9 : Basic anatomy of the electron microscope [Anchi Cheng, NYSBC] [pdf AC] Jan 14 : Challenges in biological EM & Sample Prep and practical [SEMC staff, NYSBC] [pdf EE] Jan 16 : Support films and practical [SEMC staff, NYSBC] [pdf MR YZT EE] Jan 21 : No class – Martin Luther King Jr. Holiday
Jan 23 : Fourier transforms and Image Formation [Lorenzo Finci, NYSBC] [pdf LF]

Tomography section
Jan 28 : Tomography (part I: Intro and overview of ET) [Wei Dai, Rutgers] [pdf WD] Feb 4 : Tomography (part II: FIB-SEM) [Bill Rice, NYSBC] [pdf WR] Feb 11 : Tomography (part III: Cryo-Applications & Sub-tomogram averaging) [Alex Noble, NYSBC] [pdf AN] Feb 18 : No class – President’s Day

Single particle section
Feb 25 : Single-particle analysis (part I: Intro and overview of SPA) [Joachim Frank, COLU] [pdf JF] Mar 4 : Single-particle analysis (part II: Data Analysis and reconstruction workflow [Reza Khayat, CUNY] [pdf RK] Mar 11 : Single-particle analysis (part III: Reconstruction workflow (cont), and Interpretation and Limitations) [Rich Hite, MSKCC] [pdf RH]

EM crystallography section
Mar 18 : MicroED and 2D crystallography intro [Bill Rice, NYSBC] [pdf WR] Mar 25 : Helical (part I: Intro and overview of helical) [Greg Alushin, RU] [pdf GA] Apr 1 : Helical (part II: Helical cont) [Hernando Sosa, AECOM] [pdf HS]

EM challenges and new frontiers
Apr 8 : Validation methods [Tom Walz, RU] [pdf TW] Apr 15 : EMDataBank: Structure Data Archiving, Validation Challenges [Cathy Lawson, Rutgers] [CL pdf] Apr 22 : Moderate resolution interpretation [Gira Bhabha & Damien Ekiert, NYU] [GB-DE pdf] Apr 29 : Fitting Atomic Models [Oli Clarke, COLU]  [pdf OC] May 1 : Conclusion & open discussion (short class)

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

EM fundamentals
Jan 30
Feb 6

Feb 13
Feb 20

Single Particle
Feb 27
Mar 6
Mar 13

EM crystallography
Mar 20
Mar 27
Apr 3

EM challenges and new frontiers
Apr 10 (no Journal Club)
Apr 17
Apr 24

Course instructors:

Edward Eng (NYSBC, Manager): Course leader
Laura Yen (NYSBC, Scientist): Course instructor
Yong Zi Tan (COLU, Graduate student): Teaching assistant
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)

  • 30 min 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.
  • 15 min Coffee break/informal conversation
  • 45 min Open ended discussion on the topic. Conversation starters may come from concept check questions on the topic or presentation on newerdevelopments 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