The Winter-Spring 2023 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. In the first class, we will poll the students on how to customize this course to ensure we cover the key questions they may have. Each week SEMC staff lead discussions on the practice of solving molecular structures by electron microscopy.

Course Schedule

Classes in SEMC or NYSBC seminar rooms (Winter course: Mondays 4-5pm and Wednesdays 4-5pm | Practicals may start earlier to continue later | Short course weeks: 9:00am-11am)

EM fundamentals section

Jan 9 Lecture Intro & redefining the course Ed Eng (NYSBC) [pdf]
Jan 11 Recitation Basic anatomy of the electron microscope Ed Eng (NYSBC) [pdf]
Jan 16 no class Martin Luther King Jr Holiday
Jan 18 Practical: TEM introduction: autoloaders 3-4pm sec A
4-5pm sec B[worksheet]
Jan 23 Lecture New cryoEM hardware and supporting a facility Michael Alink (NYSBC)[pdf]
Jan 25 Lecture
Sample prep vitrification – overview, grids and support films, tips and tricks when going into cryoEM, RT vs cryo
Ed Eng (NYSBC) [pdf]
Jan 30 Practical: chameleon demo 3-4pm sec A
4-5pm sec B[worksheet]
Feb 1 Recitation Roundtable (on various topics) Ed Eng (NYSBC) [pdf]

Single Particle Analysis

Feb 6 Lecture Introduction to SPA & cryoEM history
Joachim Frank (Columbia University, Note: Zoom lecture) [pdf]
Feb 8 Recitation Image formation and data collection considerations Ed Eng (NYSBC) [pdf]
Feb 13 Lecture Data Processing (more on theory and algorithms)
Amedee des Georges (CUNY/ASRC) [pdf]
Feb 15 Recitation Validation methods  Ed Eng (NYSBC) [pdf]
Feb 20 no class President’s Day Holiday
Feb 22 Recitation Roundtable (on various topics)
Zephan Melville & Mahira Aragon (NYSBC)

EM challenges and new frontiers

Feb 27 Practical cryoSPARC locally lead
Mar 1 Recitation Journal Club cryoSPARC – 3D variability
Mar 6 Practical cryoEDU workshop guest lecture by [pdf]
Mar 8 Practical TOPAZ workshop led by Alex Noble, SEMC/NYSBC [outline pdf][slides pdf]
Mar 13 Recitation Journal Club Time resolved EM
Mar 15 Recitation Journal Club Preferred orientation
Mar 20 Practical: Coot workshop – Fitting atomic models (part 1 of 2) led by Christina Zimanyi, SEMC/NYSBC [outline pdf]
Mar 22 Practical: Coot workshop – Fitting atomic models (part 2 of 2) led by Christina Zimanyi, SEMC/NYSBC
Mar 27 Recitation Journal Club Live cell imaging
Mar 29 Recitation Journal Club Time resolved EM (part 2)
Apr 3 Recitation Journal Club HIV trimer controversy
Apr 5 Recitation Wrap up 4x15min sections (1: kitchen sink, 2:)

Tomography section

April 10-14 : Short course Keynote – Intro to Tomography

See the tomography short course here. Students that attend the full course will be allowed to participate in the morning lectures.

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
Mahira Aragon (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)

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