Courses & Labs

The Electron Microscopy Core Facility provides one-on-one training for both SEM and TEM, as well as data analysis and processing. Please contact a core staff to be trained. Furthermore, we host courses and laboratory sections.

Information for students

Participating students will be introduced to biological TEM and SEM with a special emphasis on sample preparative methods.  All students will pursue individual projects and will be able to get some hands-on experience by imaging their own specimen utilizing our electron microscopes.



Funding suspended as of 2018.

This course will introduce and familiarize students with the steps required to obtain 3D information related to protein structure. Included is general TEM operation, introduction to negative staining and variables affecting results, introduction to image processing, 2D & 3D alignment, classification and averaging, plunge freezing vitreous protein samples, and collecting cryo-TEM data. The class culminates with students applying their new found knowledge to their proteins of interest with 2-3 weeks for individual projects. Students gain up to 15 hours of TEM time throughout the course.

  • Syllabus (2018)
  • Lecture1 (2018)
  • Lectures (2016)
  • Labs (2016)


Funding suspended as of 2018.

The Electron Microscopy Core Facility’s premier course for understanding theory behind and operation of electron microscopes. Lectures contain theory behind imaging and microanalysis with both scanning and transmission electron microscopes, laboratories demonstrate theory by hands-on operation of scanning (5 labs) and transmission (3 labs) electron microscopes ulitizing various imaging modes (high resolution imaging, secondary & backscattered imaging, variable pressure SEM, energy filtered imaging, STEM) with focus on microanalysis including X-ray energy dispersive spectroscopy (EDS), electron energy loss spectroscopy (EELS), energy filtered imaging (EFTEM), high angle annular dark field scanning transmission electron microscopy (HAADF STEM). Students will propose, perform and present novel imaging and microanalysis related to their research.

  • 2016 Syllabus
  • Lab 1. Introduction to SEM
  • Lab 2. Secondary and Backscattered Electron Signals
  • Lab 3. High Resolution SEM
  • Lab 4. Low Vacuum Mode in Environmental SEM
  • Lab 5. X-ray Energy Dispersive Spectroscopy for SEM
  • Lab 6. Introduction to TEM; Direct Alignments and HRTEM imaging
  • Lab 7. Scanning Transmission Electron Microscopy and X-ray Energy Dispersive Spectroscopy
  • Lab 8. Energy Filtered Imaging and Spectroscopy


Funding suspended as of 2012.

This course covers the theory and methodology to quantitatively analyze materials using both energy-dispersive (EDS) and wavelength-dispersive (WDS) spectrometry. Other topics include chemical mapping and data extraction using image processing and analysis techniques.

Over 4 days, participants in the “Nanoscale Imaging and Analysis” workshop will receive in-depth theory related to transmission electron microscopy and related analytical components available on the state’s most powerful transmission electron microscope (FEI Tecnai F30 G2 Twin). Material covered includes components, alignment and operation, image formation, high resolution TEM (HRTEM), high angle annular dark field scanning TEM (HAADF STEM), X-ray energy dispersive spectroscopy (XEDS), electron energy loss spectroscopy (EELS) and energy filtered imaging (EFTEM). After each morning’s lecture (~2 hours), students are paired and guided through hands-on operation to demonstrate the morning lecture’s theory (~2 hours) for a total of > 6 hours. The final day is reserved for students to perform individual imaging and microanalysis on their own specimens.

  • Lecture 1: TEM Basics: Theory
  • Lecture 2: TEM Basics: Alignment and Operation
  • Lecture 3: Introduction to High Resolution Transmission Electron Microscopy 
  • Lecture 4: Scanning Transmission Electron Microscopy and X-ray Energy Dispersive Spectroscopy
  • Lecture 5: Energy Filtered Imaging and Analysis
  • F30 Lab Manual