Principles and Techniques of Transmission Electron Microscopy

BIOL/MBIO/PBIO 5364 – Tentative Syllabus – Fall 2013

Samuel Roberts Noble Microscopy Laboratory 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   NML room 212

Laboratory:  TBD, TEM:  NML room 203


Textbooks for Reference (choose one, depending on research interests):


Material Sciences: 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 - 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)


Biological Sciences: 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 10/18/13)





Week 1

Aug. 19

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

Aug. 21

Instrument, Gun, and Optical Principles (PL)

Aug. 23

Instrument, Gun, and Optical Principles (PL)

Week 2

Aug. 26

Electromagnetic Lenses & Optics (SR)

Aug. 28

Electromagnetic Lenses  & Optics (SR)

Aug. 30

Instrument Training Session #1 (GS)

Week 3

Sep. 2

Labor Day

Sep. 4

Instrument Training Session #2 (GS)

Sep. 6

Instrument Training Session #3 (GS)

Week 4

Sep. 9

Vacuum Systems & Technology (PL)

Sep. 11

Vacuum Systems & Technology (PL)

Sep. 13

Electron Sources (PL)

Week 5

Sep. 16

Materials Specimen Preparation (PL)

Sep. 18

Support Film, Replicas, Shadow Casting (SR)

Sep. 20

Life Sciences Prep / Ultramicrotomy (SR)

Week 6

Sep. 23

Beam Specimen Interactions (PL)

Sep. 25

Exam 1

Sep. 27

Individual Class Projects

Week 7

Sep. 30

Energy Dispersive Spectroscopy (PL)

Oct. 2

Energy Dispersive Spectroscopy (PL)

Oct. 4

Freezing Technologies/Freeze Fracture (SR)

Week 8

Oct. 7

End Fracture/Cryoultramicrotomy (SR)

Oct. 9

Image Interpretation and Artifacts (SR)

Oct. 11

Dallas Football Weekend

Week 9

Oct. 14

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

Oct. 16

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

Oct. 18

High Voltage EM (SR)

Week 10

Oct. 21

Quantitative Microscopic Analysis and Stereological Methods (SR)

Oct. 23

Electron Tomography (SR)

Oct. 25

High Resolution TEM (PL) 

Week 11

Oct. 28

Electron Energy Loss Spectroscopy (PL)

Oct. 30

Demo: Digital Imaging (GS)

Nov. 1

Exam 2

Week 12

Nov. 4

Nov. 6

Nov 8

OAS Fall Meeting @ Cameron University

Weeks 13-16

Nov. 11-Dec 6

Poster Making /
Devoted to Completion of Projects


Fall 2013 Academic Calendar:


Final Examination Schedule and Rules: 



The goal of the course, Transmission Electron Microscopy (TEM), is to develop within students appreciation and operational ability to conduct independent research using a transmission electron microscope as well as an understanding of the principles underlying and preparation of materials for observation using TEM.  This course combines study of physical and optical principles underlying TEM, as well as hands-on training, operational procedures, basic trouble-shooting and alignment of the Zeiss 10 TEM.  As part of the course, each student will conduct a research project using a transmission electron microscope and preparatory equipment in the NML to prepare their own material.  The course will be graded by the student’s ability to take written examinations, focus and stigmation of model specimens, demonstrate practical and operational knowledge of the operation of the transmission electron microscope through written and oral examinations including operation and trouble-shooting, and presenting their research results in a poster and class presentation.  At the end of the course, the student will have practical and applied knowledge of transmission electron microscopy in the physical and biological sciences and be able to prepare samples and operate a transmission electron microscope.


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

10:30 AM on Thursday, December 12, 2013

Briefly, the project involves:



Final stigmation/focus series photographs are due on or before December 6th.  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 30th with the final set due on or before December 6th.  The stigmation micrographs consist of:



Zeiss 10:  Checkouts begin on October 9th   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:

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 NML personnel.

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

Other Equipment: Users must be checked out to use expensive pieces of preparatory equipment.  Contact NML personnel for training.  To keep training consistent, non-NML 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 NML 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 NML personnel are to train individuals on the use of NML equipment.

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

Online schedule.  The sign-up sheet and schedules for the Zeiss 10 and JEOL 2000 are 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 NML personnel before scheduling equipment use.


Grading in the course will be broken down as follows:

Exam 1                                                                      20%

Exam 2                                                                      20%

Stigmation & Focus Series                                         5%

Checkouts                                                                 15%

Final Project/Poster Presentation                              40%

Total                                                                        100%


All OU students are governed by the policies of the University of Oklahoma that are currently in force.  Policies are provided online at URL: and include all associated links and references from that page.  Particularly, these include the OU Student Code ( and the Academic Misconduct Policy (, to name the two most important references.  Any and all instances of Academic Misconduct threaten the quality of students’ learning experiences and therefore are given special scrutiny by the university.

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.