The Winter-Spring 2018 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 8 : Introduction & SEMC tour [Ed Eng, NYSBC] [YouTube EE]   [pdf] Jan 10 : Challenges in biological EM & Sample Prep [Ed Eng & Kelsey Jordan, NYSBC] [YouTube EE KJ]  [pdf] Jan 15 : No class – Martin Luther King Jr. Holiday
Jan 17 : Basic anatomy of the electron microscope [Laura Kim & Ed Eng, NYSBC] [YouTube EE LK]  [pdf] Jan 22 : Fourier transforms, Image Formation [Yong Zi & Anchi Cheng, COLU/NYSBC] [YouTube YZT AC]  [pdf]

Tomography section
Jan 29 : Tomography (part I: Intro and overview of ET) [Wei Dai, Rutgers] [YouTube WD]  [pdf WD] Feb 5 : Tomography (part II: FIB-SEM) [Bill Rice, NYSBC]  [YouTube BR]  [pdf WR] Feb 12 : Tomography (part III: Cryo-Applications & Sub-tomogram averaging) [Alex Noble, NYSBC]  [YouTube AN]  [pdf AN] Feb 19 : No class – President’s Day

Single particle section
Feb 26 : Single-particle analysis (part I: Intro and overview of SPA) [Joachim Frank, COLU]    [YouTube JF]   [pdf_JF] Mar 5 : Single-particle analysis (part II: Sample preparation and data collection for SPA) [Israel Fernandez, COLU] [YouTube IF] Mar 12 : Single-particle analysis (part III: Data Analysis and reconstruction workflow[Reza Khayat, Amedee des Georges CUNY, ASRC] ) [pdf_RK_AG] [YouTube RK ADG] Mar 19 : Single-particle analysis (part IV: Reconstruction workflow (cont), and Interpretation and Limitations) [Rich Hite, MSKCC] [YouTube RH]

EM crystallography section
Mar 26 : 2D crystallography (part I: Intro and overview of 2DX) [Iban Ubarretxena, MSSM]   [YouTube IU] Apr 2 : 2D crystallography (part II: Helical) [Hernando Sosa, AECOM]  [YouTube HS]   [pdf_HS] Apr 4 : MicroED [Bill Rice, NYSBC][pdf_WR] [YouTube BR]

EM challenges and new frontiers
Apr 9 : Validation methods [Tom Walz, RU] [pdf_TW][YouTube TW] Apr 16 : EMDataBank: Structure Data Archiving, Validation Challenges [Cathy Lawson, Rutgers] [pdf_CL][YouTube CL] Apr 23 : Moderate Resolution Fitting [SEMC staff, NYSBC] [pdf_YT_EE] Apr 30 : Fitting Atomic Models [Oli Clarke, COLU] May 2 : Conclusion & open discussion (short class) [SEMC staff, NYSBC]

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

Jan 24 : Journal Club 1 [Article 01] Jan 31 : Microscopy Practical
Feb 7 : Journal Club 2 [Article 02] Feb 14 : Journal Club 3 [Article 03] Feb 21 : no recitation
Feb 28 : CryoET Basics Practical
Mar 7 : no recitation (postponed due to weather)
Mar 14 : Journal Club 4 [Article 04] Mar 21 : Cellular CryoET Practical (postponed due to weather)
Mar 28 : Journal Club 5 [Article 05] Apr 11 : Journal Club 6 [Article 06] Apr 18 : Single Particle Practical
Apr 25 : Journal Club 7 [Article 07] [Course Handbook]

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 50%
  • Practical Worksheet 10% x 4
  • Attendance 10%

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 newer developments in the field.