Principles and Techniques of Transmission Electron Microscopy

BOT/MBIO/ZOO 5364 – Tentative Syllabus – Fall 2012

Samuel Roberts Noble Electron Microscopy Web site:

SRNEML Laboratory Phone:  325-4391

D2L Class Website:



Scott Russell, GLC Professor, and Director  Office:  210 NML e-mail:

Preston Larson, Research Scientist  Office:  205E NML  e-mail:

Greg Strout, Electron Microscopist  Office:  214 NML  e-mail:


Lecture:  MWF 8:30-9:20 am

Laboratory:  TBD, TEM:  TBD


Textbooks for Reference:


Materials: D. B. Williams and C. B. Carter, “Transmission Electron Microscopy:  A Textbook for Material Scientists” (1996) Plenum Press, New York, NY.  ISBN 0-306-45247-2 (Hardcover). - OR -

Materials: D. B. Williams and C. B. Carter, “Transmission Electron Microscopy, 2nd edition” (2009) Springer Verlag, New York, NY.  ISBN 978-0-387-76500-6 (Hardcover) 837 pp. $149, 978-0-387765020 (Softcover) $99 (also Kindle Edition) (Amazon has new copes of these for $98.23 and $70.99, respectively, on 8/19/2012)


Biologicals: J. J. Bozzola and L. D. Russell, “Electron Microscopy:  Principles and Techniques for Biologists”, 2nd ed. (1999), Jones & Bartlett.  ISBN 0-7637-0192-0 (Hardcover), pp $160.95 retail. (also Kindle Edition) (Amazon has new copies at retail as of 9/28/12, used are less)




Tentative Course Schedule (as of 10/28/12)





Week 1

Aug. 20

Course content, requirements, grading, lab rules, lab tour, Intro to Electron Microscopy (SR)

Aug. 22

Instrument, Gun, and Optical Principles (PL)

Aug. 24

Instrument, Gun, and Optical Principles (PL)

Week 2

Aug. 27

Electromagnetic Lenses & Optics (SR)

Aug. 29

Electromagnetic Lenses  & Optics (SR)

Aug. 31

Instrument Training Session #1 (GS)

Week 3

Sep. 3

Labor Day

Sep. 5

Instrument Training Session #2 (GS)

Sep. 7

Vacuum Systems & Technology (PL)

Week 4

Sep. 10

Vacuum Systems & Technology (PL)

Sep. 12

Electron Sources (PL)

Sep. 14

Materials Specimen Preparation (PL)

Week 5

Sep. 17

Support Film, Replicas, Shadow Casting (GS)

Sep. 19

Life Sciences Prep / Ultramicrotomy (SR)

Sep. 21

Beam Specimen Interactions (PL)

Week 6

Sep. 24

Exam 1

Sep. 26

Individual Class Projects

Sep. 28

Energy Dispersive Spectroscopy (PL)

Week 7

Oct. 1

Energy Dispersive Spectroscopy (PL)

Oct. 3

Freezing Technologies/Freeze Fracture (SR)

Oct. 5

End Fracture/Cryoultramicrotomy (SR)

Week 8

Oct. 8

Image Interpretation and Artifacts (SR)

Oct. 10

Demo: Digital Imaging (GS)

Oct. 12

Dallas Football Weekend

Week 9

Oct. 15

TEM Imaging Modes: Imaging Principles, Resolution, Ray Paths (PL)

Oct. 17

TEM Imaging Modes: Diffraction, Bright Field, Dark Field, STEM, HAADF (PL)

Oct. 19

High Resolution TEM (PL)

Week 10

Oct. 22

Electron Energy Loss Spectroscopy (PL)

Oct. 24

Check-out Written Exam

Oct. 26

High Voltage EM (SR)

Week 11

Oct. 29

Quantitative Microscopic Analysis and Stereological Methods (SR)

Oct. 31

Electron Tomography (SR)

Nov. 2

Exam 2

Week 12

Nov. 5

No Class

Nov. 7

No Class

Nov 9

OAS Fall Meeting @ UCO

Weeks 13-16

Nov. 12-Dec 7

Poster Making /
Devoted to Completion of Projects


Fall 2012 Academic Calendar:

Final Examination Schedule and Rules: 



Projects are presented in lieu of a final examination.  All projects are due at the final:

10:30 AM on Tuesday, December 11, 2012


Briefly, the project involves:


  • A poster suitable for a scientific meeting.  The poster has a Title, Abstract, Introduction, Experimental Procedures, Results, Discussion, Conclusions, Literature Cited.  There will be a minimum of 4 TEM micrographs of 4” x 5” or larger on the poster, provided with a scale bar on the micrograph and the magnification listed in the figure legend.  Corresponding negatives for these images (or a corresponding scanned negative) should be handed in with the poster. 
  • A 10-15 minute oral presentation explaining the project and poster.  The oral presentation should include sufficient introductory information that the audience gains an understanding of the scientific significance of the project.  The audience may be provided with critique sheets.
  • Poster guidelines will be discussed in class.





Final stigmation/focus series photographs are due on or before December 10th.  Up to three sets of stigmation/focus series images may be turned in and only the highest grade will count.  The first set will be due on October 28th with the final set due on or before December 10th.  The stigmation micrographs consist of:


  • Using a holey carbon grid to take three stigmated images at overfocus, focus, and underfocus of a hole at 125,000´.




Zeiss 10:  Checkouts begin on October 10th


Check-outs may include both a written and oral/hands-on component.  The length of an individual student’s checkout is variable depending on their knowledge of the microscope, principles of electron microscopy and operational skill, but plan on allotting around 4-6 hours.  Checkouts on both TEMs will consist of the following parts:


  • System Description
  • Operation and Alignment
  • Trouble-shooting


If a need exists for you to use the JEOL 2000FX (e.g. higher resolution), consult the instructor to discuss the possibility of training on this machine.  Training on the JEOL 2000FX will be based on research needs, competence (partly based on the Zeiss 10 checkouts), time constraints, and the discretion of EML personnel.


JEOL 2000FX:  Checkouts will be conducted at the discretion of EML personnel.


Other Equipment: Users must be checked out to use expensive pieces of preparatory equipment.  Contact EML personnel for training.  To keep training consistent, non-EML personnel are not permitted to conduct separate training.  Supervised operation is required until you are competent and checked out.


User’s List:  A list of users of EML equipment and the instruments they are qualified to use is maintained by the lab.  DO NOT USE any equipment on which you have not been checked out.  Only EML personnel are to train individuals on the use of EML equipment.


Note:  It is recommended that you begin working on your project prior to completing your checkout.


Online schedule.  The sign-up and schedule for the Zeiss 10 and JEOL 2000 is located online at:


You will be entered into the system when you become knowledgeable and independent enough to use the microscope without EM personnel present.  Consult EML personnel before scheduling equipment use.



Grading in the course will be broken down as follows:

Exam 1                                               20%

Exam 2                                               20%

Stig Series                                            5%

Checkouts                                         15%

Final Project/Poster Presentation 40%

Total                                                  100%




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All of these stated policies are incorporated into this syllabus by this reference.  It is ultimately the student’s responsibility to be aware of current and changing policies over the course of their academic career.  All participants in the course are bound by these policies.