Light and Video Microscopy
Randy Wayne (255 8904; row1@cornell.edu; 203 Plant Sciences Bldg.)
Fall 2012, 248 Pl. Sci. Bldg. Lecture: TR 1:25-2:40; Lab T 2:45-4:25
Date
Lecture
Laboratory
August 23
August 28
August 30
The Relation between the Object and the Image
Geometrical Optics: Mirrors
Geometrical Optics: Lenses
Nature of Light
Geometrical Optics
September 4
Physical Optics: Diffraction
September 6
Physical Optics: Resolution
Physical Optics
September 11
Bright Field Microscopy
September 13
Photomicrography
Bright Field Microscopy
September 18
Phase Contrast and Dark Field Microscopy
Rheinberg and Oblique Illumination
September 20
Fluorescence Microscopy
Phase Contrast and Dark
Field Microscopy
September 25
Polarization Microscopy
September 27
Polarization Microscopy
Fluorescence Microscopy
October 2
Polarization Microscopy
October 4
Polarization Microscopy
Fluorescence and
Polarization Microscopy
October 6-9
Fall Break
October 11
Interference Microscopy
Polarization Microscopy (IM)
Take-home Prelim Due (300 pts)
October 16
Interference Microscopy
October 18
Differential Interference Microscopy (DIC) Interference Microscopy
October 23
Modulation Contrast Microscopy (HMC)
October 25
Video and Digital Microscopy
DIC and HMC Microscopy
October 30
Analog Image Processing
November 1
Digital Image Processing
Video Microscopy and
Image Processing
November 6
Laser Microscopy
November 8
Miscellaneous Microscopes and Accessories Confocal Microscopy
(We will meet at the Plant Cell Imaging Center (PCIC) Room 104B, Boyce Thompson Institute
for Plant Research (BTI) from 12-2 PM)
November 13
Free Time to Work on Projects
November 15
Free Time to Work on Projects
November 20
Free Time to Work on Projects
November 21-25
Thanksgiving Break
November 27
Rare Book Library Visit
November 29
Presentations of Research Projects (Could be Moved to Final Exam Time)
Textbook: Light and Video Microscopy by Randy Wayne (Royalties go to Habitat for
Humanity)
Getting Help:
Feel free to come and discuss material with me in 203 Pl. Sci. Bldg. My email address is
row1@cornell.edu and my telephone number is 255 8904.
Expectations:
Please read the lecture material before coming to lecture and the laboratory material before
coming to lab. The lab will concentrate on giving you hands on experience with some of the
concepts and methods discussed in lecture. Try to integrate the two parts of the course.
Lecture Grades:
There will be one written take-home prelim exam (300 pts) and one final paper. The final paper
will be a creative writing story (300 pts). A component of the lecture grade will be subjective
based on your conduct and preparedness.
Lab Grades:
There will be two basic components: a video project and a research project. These will be
presented to the class at the end of the semester. A component of the lab grade will be subjective
based on your conduct and preparedness.
Research:
Video Project (100 pts)
Make a 5 minute video of a specimen or a process that takes advantage of video or digital
microscopy in studying the movements that occur in microscopic objects (e.g. chloroplast
rotation and other chloroplast movements, embryo development, cytoplasmic streaming,
phagocytosis, flagellar movement, etc.). Write up a one or two page paper that describes the
organism and process you are studying and the type of optics and video equipment you are using.
Research Project (300 pts)
Choose a project where an important or interesting question can be answered using the
techniques of light microscopy you have learned this semester. Discuss your project with me by
the first or second week of November. Let me know what equipment you will need for your
project.
You must present your research project both as a 15 minute oral Powerpoint presentation to the
class and as a written report that includes (1) an Introduction that states what the project entails,
what questions you are asking and why you chose the type of microscopy you used; (2) a
Materials and Methods section that explains in detail the material and methods you used to that
anyone could repeat your work; (3) a Results and Discussion section where you present your
data as photographic prints, describe your data and give conclusions about the appropriateness of
the methods you chose, the problems you encountered, how you could so the project better next
time, the answers to the questions you asked in the introduction, and new questions that came up
as a result of the study; and (4) References. The written report should be about 4-5 pages.
Feedback:
Please feel free to give any comments or suggestions you might have concerning how this course
may be taught more effectively.
Academic Integrity:
College is a time for you to find and develop your character, interests and skills. I expect that you
will be described as someone who is honest. The Cornell University Code of Academic Integrity
states that, “Absolute integrity is expected of every Cornell student in all academic undertakings.
Integrity entails a firm adherence to a set of values, and the values most essential to an academic
community are grounded on the concept of honesty with respect to the intellectual efforts of
oneself and others. Academic integrity is expected not only in formal coursework situations, but
in all University relationships and interactions connected to the educational process, including
the use of University resources. While both students and faculty of Cornell assume the
responsibility of maintaining and furthering these values, this document is concerned specifically
with the conduct of students.
A Cornell student's submission of work for academic credit indicates that the work is the
student's own. All outside assistance should be acknowledged, and the student's academic
position truthfully reported at all times. In addition, Cornell students have a right to expect
academic integrity from each of their peers.”
Specific examples of code violations can be found at:
http://cuinfo.cornell.edu/Academic/AIC.html.
University Days
James Thurber
I passed all the other courses that I took at my University, but I could never pass botany. This
was because all botany students had to spend several hours a week in a laboratory looking
through a microscope at plant cells, and I could never see through a microscope. I never once
saw a cell through a microscope. This used to enrage my instructor. He would wander around the
laboratory pleased with the progress all the students were making in drawing the involved and,
so I am told, interesting structure of flower sells, until he came to me. I would be just standing
there. "I can't see anything," I would say. He would begin patiently enough, explaining how
anybody can see through a microscope, but he would always end up in a fury; claiming that I
could too see through a microscope but just pretended I couldn't. "It takes away from the beauty
of flowers anyway," I used to tell him. "We are not concerned with beauty in this course," he
would say, "We are concerned solely with what I may call the mechanics of flars." "Well," I
would say, "I can't see anything." "Try it just once again," he'd say, and I would put my eye to
the microscope and see nothing at all, except now and again a nebulous milky substance----a
phenomenon of maladjustment. You were supposed to see vivid, restless clockwork of sharply
defined plant cells. "I see what looks like a lot of milk." I would tell him. This, he claimed, was
the result of my not having adjusted the microscope properly, so he would readjust it for me, or
rather, for himself. And I would look again and see milk.
I finally took a deferred pass, as they called it, and waited a year and tried again. (You had to
pass one of the biological sciences or you couldn't graduate.) The professor had come back from
vacation brown as a berry, bright-eyed, and eager to explain cell-structure again to his classes.
"Well," he said to me, cheerily, when we met in the first laboratory hour the semester, "We're
going to see cells this time, aren't we?" "Yes, sir." I said. Students to the right of me and left of
me and in front of me were seeing cells; what's more, they were drawing pictures of them in their
notebooks. Of course, I didn't see anything.
"We'll try it," the professor said to me, grimly, "with every adjustment of the microscope known
to man. As god is my witness, I'll arrange this glass so that you see cells through it or I'll give up
teaching. In twenty-two years of botany, I----" he cut off abruptly for he was beginning to quiver
all over, like Lionel Barrymore, and he genuinely wished to hold onto his temper; his scenes with
me had taken a great deal out of him.
So we tried it with every adjustment of the microscope known to man. With only one of them did
I see anything but blackness or the familiar lacteal opacity, and that time I saw, to my pleasure
and amusement, a variegated constellation of flecks, specks and dots. These I hastily drew. The
instructor, noting my activity, came from an adjoining desk, a smile on his lips, eyebrows high in
hope. He looked at my cell drawing. "What's that?" he demanded, with a hint of squeal in his
voice. "That's what I saw." I said. "You didn't. You didn't. You didn't!" he screamed, losing
control of his temper instantly, and he bent over and squinted into the microscope. His head
snapped up. "That's your eye!" he shouted. "You've fixed the lens so that it reflects! You've
drawn your own eye!"
Reminder:
Thatige Skepsis. That is, maintain as active skepticism and do not believe anything I say. If
something does not ring true, question me and discover the truths on your own. The lab will give
you a chance to experiment with many aspects of optics and microscopy.
The following is a list of the things you must memorize for this class: