1 Halsey Science Center Rooms 156 (office) and 55 (lab)

Biology 350/550
Electron Microscopy
Course Description and Syllabus
Fall 2006
Dr. Todd A. Kostman
Halsey Science Center Rooms 156 (office) and 55 (lab)
Office phone: 424-7301
EM Lab phone: 424-0811
e-mail: kostman@uwosh.edu
Office Hours: M, W 2-4 p.m. or by appointment
I am happy to meet with you anytime that I am free, and I will make every effort to be
available. I encourage you to make appointments, as it ensures that I will available. It is
easiest to communicate with me via e-mail, as I move around the building constantly during
the day, so if you try to get me by phone, we will end up playing phone tag.
Course Description
Electron Microscopy is a comprehensive course on the fundamentals of specimen preparation,
microscope operation and the production of excellent micrographs from both the Transmission
Electron Microscope (TEM) and the Scanning Electron Microscope (SEM). Both the theory
and practice(s) of Electron Microscopy will be covered over the course of the semester during
lecture and lab periods. In a nutshell, you will learn about the principles in lecture and apply
them during lab.
Course Objectives
By the end of this semester, you should possess the following skills/knowledge:
1. Ability to prepare specimens for examination on both the TEM and SEM
2. In depth knowledge of the procedures and protocols necessary for specimen
preparation for both TEM and SEM- enough knowledge to enable you to modify
protocols according to the application.
3. Ability to operate both the TEM and SEM at the level I deem appropriate.
4. Basic knowledge of the design and mechanics of scope operation for both
5. Ability to convert raw data collected from scopes (negatives or digital images) into a
publishable form via a photo-enlarger or imaging software.
Course Materials
All lectures will be via Powerpoint, and they will be available on the D2Learn site set-up for this
course. In addition, I will post items for you to read, messages for the class, and sample
exams. I will make every effort to post the lectures at least a day prior to their delivery in
class. The posted lectures will be in outline format, and I will fill in additional details (which you
will need to know!) during the lecture period
The Laboratory: What will happen in lab? Above I have given you an outline of the topic to
be covered in lab each week. During lab, I will use a combination of lecture and
demonstration to show you a technique, we will then devote the remainder of the lab time to
practicing the technique(s), with myself present to guide you along. I must stress here that
attending lab is critical to success in the course. In extreme circumstances, I may be willing to
let you make up a missed lab, but if it does not involve a serious illness, accident, or family
emergency, you will be out of luck and have to rely on the help of your classmates. Note that
you will attend either the Tuesday or Thursday section of the lab but not both. Both sections
will be covering the same topics at the same time. If you need to attend a different section for
just one session due to a conflict please see me.
Cooperation: During the course of the lab sessions and other times, you will be working very
closely with the other members of the class. I encourage you to help each other out when it
comes of mastering the techniques, as this is a great way of learning them yourself. What I do
not want, however, are group efforts when it comes to producing negatives and prints. Feel
free to give pointers, but each of you have to do your own work.
Time Commitment: One last comment I will make is about how to succeed in this class.
Considering the amount of work, I deem it impossible to complete the assigned objectives
during class time alone. You will have to come in at other times if you want to do well. I do
restrict use of the scopes without my supervision until I have officially checked you out: once I
have done so, you can use them anytime of the day or night. All other equipment may be
used without a formal "checkout", as long as you feel comfortable using it.
Lecture and Lab Schedule-Electron Microscopy Fall 2006
Week of
Lecture Topic
Lab Exercise
Sept. 6
Introduction, History, Fixation
Lab tour, safety, split into lab groups
Sept. 13
Fixation and embedding for TEM, block trimming
Sept. 20
Dehydration and embedding for Ultramicrotomy-set-up and thick sectioning
Sept. 27
Sectioning and staining for TEM Ultramicrotomy thick sectioning; staining thick
sections for LM
Oct. 4
TEM -design
Ultramicrotomy-thin sectioning and collecting
sections on grids
Oct. 11
TEM -design
Staining thin sections, TEM Operation-alignment
Oct. 18
Exam I-Lectures 1-6
TEM operation-focusing and taking pictures
Oct. 25
TEM -image formation
SEM sample preparation/darkroom
procedures/TEM practice
Nov. 1
SEM sample preparation
SEM operation intro; TEM and SEM practice
Nov. 8
SEM operation and collection of digital images
Nov. 15
Vacuum systems
SEM operation practice
Nov. 22
No lecture-Thanksgiving break
open lab on Tuesday
Nov. 29
Photography and digital imaging SEM operation-energy dispersive X-ray
Dec. 6
EM applications, other
open lab
microscope types
Dec. 13
Second exam-lectures 6-12
open lab
Since this is a very hands-on course, much of your grade will depend upon the time and effort
you put into learning the techniques and operating the microscopes. If you put in the effort,
you will do well. I am not expecting perfection, but I do expect you to do your best. With this
in mind, the grading is weighted heavily towards my assessment of your performance of
various tasks related to specimen preparation, scope operation, and production of final
images. There will be two lecture exams, one at mid-term and one at the end of the semester
to test your conceptual understanding.
Graded Item
Due Date
Trimmed blocks
Stained and cover slipped thick sections
Lecture Exam I
Stained thin sections
TEM Checkout and Operation
SEM Checkout and Operation
Turn in 2 TEM negs and prints
Turn in 2 SEM digital images
Collection of an EDS Spectrum
Exam II
Micrographs and negatives, TEM
SEM Plate
SEM Digital Images
Oct. 6
Oct. 20
Oct. 18
Oct. 27
Nov. 10
Dec. 1
Dec. 1
Dec. 1
Dec. 15
Dec. 13
Dec. 15
Dec. 15
Dec. 15
Grading Scale: I will take the number of points you earn out of and divide by 800 to obtain a
percent value. I will then apply the standard 90-100=A, 87-89=A/B etc. scale to determine
your letter grade. Grading sheets for each of the exercises are located in your lab notebook
and need to be turned in as the items are turned in to be graded. I will then return the sheet
and graded items to you.
Additional information on the grading criteria for each above item:
1. Trimmed blocks: You will hand in three trimmed blocks; I will grade the best 2 of the 3 for
10pts each. What I will be looking for is shape of block face, sized of block face, height of
block face (no monoliths…you will see what I mean), smoothness of the sides of the block
face, and slope of the sides.
2. Stained and cover-slipped thick sections: You will hand in two slides, each with at least
three sections, stained with any LM stain of your choosing. I will grade the best section on
each slide, in terms of tissue quality/preservation, quality of staining/contrast, overall quality of
the section. Each section will be thus worth 10pts.
3. Stained thin sections: You will hand in 2 grids on which will be hopefully at least 2 thin
sections, which have been post-stained with calcined lead stain. I will grade two sections, one
from each grid, on the basis of staining quality, section quality, tissue quality, and section
4. TEM checkout: On or before the due date, I will sit down with you on the TEM and observe
and grade your ability to insert a specimen, saturate the beam, align the beam, align the
objective aperature, change magnification, stigmate the objective lens at 100,000X, focus, and
shoot a negative.
5. SEM checkout: On or before the due date, I will sit down with you on the SEM and observe
and grade your ability to insert a specimen, turn in the beam, turn up the filament, obtain and
initial image, saturate the filament, change the working distance, to up to a magnification of
10,000x, focus, stigmate, adjust brightness and contrast, collect a high-resolution image at
2,000x, and produce a photo printer printout of the image.
6. Collection of an EDS Spectrum: On or before the due date, I will give you a sample of
unknown composition, and you will have to insert the specimen, set-up the scope properly,
and use the EDS software (Vantage) to collect a spectrum that will identify the element(s)
present in the sample.
Micrographs negatives, and digital images: What you will turn into me as your final "work"
in the course will determine over 50% of your grade. What will you turn in? Good question. I
will break it down into what you will turn in for the TEM and the SEM:
7. TEM:
You will turn in 8 negatives and 8 prints made via the photographic enlarger. The prints need
to be at least 4”x6”. At least two of the negatives must be taken at a magnification above
30,000X. When I grade the negatives, I am looking to see if the image is in focus, if the
amount of contrast is sufficient, if the image is actually of some cell or tissue, and if the
negative was developed properly. For the prints, I am looking to see if the image is focused, if
the amount of contrast is appropriate, and I also evaluate the overall quality of the image. Note
that you will turn in two of the negatives and prints two weeks prior to the end of the
semester...on these I can give you feedback so that you can improve the remaining images
that you turn in.
8. SEM:
You will be turning in a total of 10 images collected using the SEM and the Vantage Digital
Imaging Software. What I would like you to do is take four of the images and turn them into a
photographic plate, complete with micron bars and labels. This you will print out (on glossy
paper) on one of the inkjet printers available in the lab. The other six images you will turn in as
TIFF files saved to a folder on the desktop of the SEM computer. At least two of the SEM
images must be acquired at above 10,000X. The other eight images can be at any
magnification. You may put the above 10,000X images in the plate, or you can turn them in as
TIFF’s, I leave that up to you. I will provide training on how to do all of the above, so don’t
freak out yet. For all of the SEM images, I will be looking at the same criteria as for the TEM
negatives and prints. As with the TEM images, you will turn in two digital images to me two
weeks prior to semester’s end. These I will grade so that you can improve your SEM plate
and final digital images.
Academic dishonesty
Students are referred to the University of Wisconsin Oshkosh Student Discipline Code as
detailed in specific provisions of Chapter 14 of the State of Wisconsin Administrative Code.
Any student(s) found in violation of any aspect of the above Code (as defined in sections UWS
14.02 and 14.03) will receive a sanction as detailed in UWS 14.05 and 14.06. Examples of
violations include: looking at another student’s exam or answer sheet and copying the answers
during and exam, talking or whispering to another student during an exam and receiving text
messages during an exam on an electronic device. Sanctions range from a grade of zero for
the assignment in question to an oral reprimand to expulsion from the University of Wisconsin
Oshkosh. Students have the right to request a hearing and to appeal sanctions (as defined in
UWS 14.08-14.10).