The Winter-Spring 2017 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 9 : Introduction & SEMC tour [SEMC staff, NYSBC][pdf EE] Jan 11 : (Video Screenings for introductory lectures)
Jan 16 : No class – Martin Luther King
Jan 18 : Challenges in biological EM & Sample Prep [Ashleigh Raczkowski/Kelsey Jordan & Ed Eng, NYSBC] [pdf AR-KJ] Jan 23 : Basic anatomy of the electron microscope [Laura Kim/Anchi Cheng & Ed Eng, NYSBC] [pdf] Jan 25 : Fourier transforms [Bill Rice, NYSBC] [pdf WR] Jan 30 : Image Formation [Bill Rice & Anchi Cheng, NYSBC] [pdf WR] [pdf AC]

Tomography section
Feb 6 : Tomography (part I: Intro and overview of ET) [David Stokes, NYU] [pdf DS] Feb 13 : Tomography (part II: FIB-SEM) [Bill Rice, NYSBC] [pdf WR] Feb 20 : No class – President’s Day
Feb 27 : Tomography (part III: Cryo-Applications & Sub-tomogram averaging) [Alex Noble, NYSBC] [pdf AN]

Single particle section
Mar 6 : Single-particle analysis (part I: Intro and overview of SPA) [Joachim Frank, COLU] [pdf JF] Mar 13 : Single-particle analysis (part II: Data Analysis and reconstruction workflow) [Reza Khayat, CUNY] [pdf RK] Mar 20 : Single-particle analysis (part III: Reconstruction workflow (cont), and Interpretation and Limitations) [Rich Hite, MSKCC] [pdf RH]

2D crystallography section
Apr 5 : 2D crystallography (part I: Intro and overview of 2DX) [Iban Ubarretxena, MSSM] [pdf IU] Apr 3 : 2D crystallography (part II: Helical) [Hernando Sosa, AECOM] [pdf HS]

EM challenges and new frontiers
Apr 10 : EMDataBank: Structure Data Archiving, Validation Challenges [Cathy Lawson, Rutgers] [pdf CL] Apr 17 : Validation methods [Tom Walz, RU] [pdf TW] Apr 24 : Fitting Atomic Models [Oli Clarke, COLU] May 1 : Conclusion & open discussion (short class) [SEMC staff, NYSBC]

Lecture slides from the 2016 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.

Video screenings in the SEMC conference room (usually starts @3:30pm)
Jan 11 : Basic anatomy of the electron microscope
Jan 11 : Fourier transforms and reciprocal space
Jan 11 : Image Formation
Jan 11 : Fundamental challenges in biological EM
Jan 18 : [lecture] Jan 25 : [lecture] Feb 1 : Tomography (part I)
Feb 8 : Tomography (part II)
Feb 15 : [no screening] Feb 22 : [no screening] Mar 1 : Single-particle analysis (part I)
Mar 8 : Single-particle analysis (part II)
Mar 15 : Single-particle analysis (part III)
Mar 22 : 2D crystallography

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 a recent paper.
  • 15 min Coffee break/informal conversation
  • 45 min Open ended discussion covering concept check questions on the topic