Principles and Techniques of Transmission
Electron Microscopy
MBIO 5364 – Tentative
Syllabus – Fall 2018
Samuel
Roberts Noble Microscopy Laboratory Web site:
http://www.microscopy.ou.edu/
SRNML Laboratory Phone:
325-4391
Canvas Class Website:
Instructors:
Scott Russell, GLC
Professor, and Director
Office:
210 NML e-mail: srussell@ou.edu
Preston Larson, Research Scientist Office:
205E NML e-mail: plarson@ou.edu
Lecture: MWF 8:30-9:20 am NML room 212
Laboratory:
TBD, TEM:
NML room 203
General Textbook for All Students in the
Class:
Physical
Principles of TEM: Ray F. Egerton. “Physical Principles of
Electron Microscopy An Introduction to TEM, SEM, and AEM (2005) Springer, New York, NY is available free on OU sites at URL: https://link.springer.com/book/10.1007%2Fb136495
or in hardcover through book sellers ISBN: 978-0-387-25800-3 (Print)
Specialized Textbooks for Specialized
Applications/Techniques (choose one, depending on research interests):
Material
Sciences: D. B. Williams and C.
B. Carter, “Transmission Electron Microscopy:
A Textbook for Material Scientists, 2nd edition” (2009) Springer, New
York, NY is available free on OU sites at URL: http://link.springer.com/book/10.1007%2F978-0-387-76501-3
or in hardcover through book sellers ISBN 978-0-387-76500-6 (Hardcover) 837 pp.
~$149, 978-0-387765020 (Softcover) $99.
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 $145.00 retail. (Amazon used copies were about the same as
retail as of 8/2/17, but some content is available free at
http://books.google.com/ (search for ISBN 0-7637-0192-0 for an exact match).
Tentative Course Schedule (as of 8/20/18)
|
Week |
Date |
Lecture |
|
Week 1 |
Aug. 20 |
Course content,
requirements, grading, lab rules, lab tour, Intro to Electron Microscopy (SR) |
|
Aug. 22 |
Instrument, Gun, and
Optical Principles (SR) |
|
|
Aug. 24 |
Vacuum Systems &
Technology (SR) |
|
|
Week 2 |
Aug. 27 |
Vacuum Systems &
Start Optical Prin (SR) |
|
Aug. 29 |
Instrument Training
Session #1 (SR) |
|
|
Aug. 31 |
Instrument Training
Session #2 (SR) |
|
|
Week 3 |
Sept. 3 |
Labor Day |
|
Sept. 5 |
Electromagnetic
Lenses & Optics (PL) |
|
|
Sept. 7 |
Electromagnetic
Lenses & Optics (PL) |
|
|
Week 4 |
Sept. 10 |
Life Sciences Prep /
Ultramicrotomy (SR) |
|
Sept. 12 |
Support Film,
Replicas, Shadow Casting (SR) |
|
|
Sept. 14 |
Materials Specimen Preparation
(PL) |
|
|
Week 5 |
Sept. 17 |
Electron Sources (PL) |
|
Sept. 19 |
Beam Specimen
Interactions (PL) |
|
|
Sept. 21 |
High Voltage EM (SR) |
|
|
Week 6 |
Sept. 24 |
Completion of Above
Topics and Review |
|
Sept. 26 |
Exam 1 (Room 40 in GLCH) |
|
|
Sept. 28 |
Individual Class Projects |
|
|
Week 7 |
Oct. 1 |
Imaging and
Introduction to Interpretation (SR) |
|
Oct. 3 |
Image Interpretation
and Artifacts (SR) |
|
|
Oct. 5 |
Electron Tomography
(SR) |
|
|
Week 8 |
Oct. 8 |
Freezing
Technologies/Freeze Fracture (SR) |
|
Oct. 10 |
End Fracture/Cryoultramicrotomy (SR) |
|
|
Oct. 12 |
Dallas Football
Weekend (no class) |
|
|
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 |
Energy Dispersive Spectroscopy
(PL) |
|
|
Week 10 |
Oct. 22 |
Energy Dispersive
Spectroscopy (PL) |
|
Oct. 24 |
Digital Imaging (PL) |
|
|
Oct. 26 |
High Resolution TEM (PL) |
|
|
Week 11 |
Oct. 29 |
Electron Energy Loss
Spectroscopy (PL) |
|
Oct. 31 |
Quantitative
Microscopic Analysis and Stereological Methods (SR) |
|
|
Nov. 2 |
OAS Fall Meeting @
Rogers State University, Claremore, OK |
|
|
Week 12 |
Nov. 5 |
Completion of Topics
and Review for Exam 2 |
|
Nov. 7 |
Exam 2 (Room 40 in GLCH) |
|
|
Nov 9 |
||
|
Weeks 13-16 |
Nov 12-Dec 14 |
Poster Making / |
Fall
2018 Academic Calendar:
http://www.ou.edu/content/admissions/academic_calendar/fall-2018.html
Final Examination Schedule
and Rules:
http://www.ou.edu/content/enrollment/final_exams.html
INSTRUCTIONAL GOALS OF THE COURSE
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.
FINAL PROJECTS
Projects
are presented in lieu of a final examination.
All projects are due at the final:
10:30
AM on Thursday, December 13, 2018
Briefly,
the project involves:
- A
poster suitable for a scientific meeting.
The poster has a Title, Abstract, Introduction, Experimental
Procedures, Results, Discussion, Conclusions and Literature Cited. There will be a minimum of 4 TEM micrographs of 5” 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.
STIGMATION MICROGRAPHS
Final stigmation/focus
series photographs are due on or before December 7th. Up to three sets of stigmation/focus
series images may be turned in and only the highest grade will count. The first set will have a target due date of October 31st with the second
target date of November 17 and final
set due on December 7th. The stigmation
micrographs consist of:
- Using
a holey carbon grid to take three stigmated images at 80KV on
the Zeiss 10 at (1) overfocus, (2) true
focus, and (3) optimum underfocus of a hole at 125,000´.
These should be scanned at 1200 dpi according to Greg’s parameters
for using the scanner.
- REQUIREMENTS:
- Images
must use gray scales of at least 170 gray shades.
- All
images MUST include the negative image number (all five numbers), KV and
magnification setting.
- All
images should be clearly labeled as overfocus,
true focus and optimum underfocus.
- Each
student must do the entire focus and stig
series separate from their partner and all other students.
- For submission by
email:
Image copies for submission should be reduced to 300 dpi and converted to JPGs at high
quality. This will yield images
that are about 3500 x 4400 pixels and will be <3 MB each so that within
OU email, they are small enough to be delivered
reliably.
EQUIPMENT CHECK-OUT
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:
- 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 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: http://www.microscopy.ou.edu/schedule/index.cgi
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
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%
POLICY
All OU students are
governed by the policies of the University of Oklahoma that are currently in
force. Policies are provided online at
URL: http://catalog.ou.edu/current/Policies.htm
and include all associated links and references from that page. Particularly, these include the OU Student Code (http://www.ou.edu/content/dam/studentlife/documents/AllCampusStudentCode.pdf)
and the Academic Misconduct Policy (http://integrity.ou.edu/),
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.