Biology 333/433 Advanced M icroscopy Techniques, Tentative Syllabus, Spring, 2013
Date
Topic
Reference
Text
General
Reference:\primer\index.html :
Jan 22
Introduction, properties of light.
Resolution
General Properties of
Light:\primer\lightandcolor\inde
x.html
Chapter 2,
Chapter 5
Resolution:\www.microscopyU.
com\articles\formulas\formulasre
solution.html
Jan 24
Refraction, Image formation by
convex lenses
Refraction:\primer\lightandcolo
r\refraction.html
Convex
Lenses:\primer\lightandcolor\len
sesintro.html
Jan 29
Convex lenses, continued, Lens
Aberrations - Spherical,
chromatic, etc-
Lenses:\primer\java\lenses\conv
erginglenses\index.html
Aberrations:\primer\anatomy\ab
errationhome.html
Chapter 4
Chapter 4
continued
\primer\anatomy\components.ht
ml
Fixed Tube Length:
\primer\java\components\fixedtu
belength\index.html
Infinity Tube Length:
\primer\java\components\infinity
microscope\index.html
Jan 31
aberrations redux, the
enlargement system of a
microscope, microscope
objectives. Kohler Illumination,
Inverted microscope
Objectives:\primer\anatomy\obj
ectives.html
\primer\anatomy\specifications.h
tml
Role of immersion oil:
\primer\java\microscopy\immersi
on\index.html
Condenser Illumination:
\primer\java\components\conden
ser\index.html
Koehler Illumination:
\primer\anatomy\kohler.html
Chapter 1
Lab 1.
(Feb 5-7)
Feb 5
Lab Exercise on elements of the
light microscope - room 348
Oculars, More on conjugate
planes, the objective back focal
plane.
Handouts, "Diffkit" program on
course disk.
Oculars:
\primer\anatomy\oculars.html
Image
Formation:\primer\anatomy\ima
ge.html
Chapter 1
Contrast:\www.microscopyU.co
m\articles\formulas\specimencon
trast.html
Phase Objects:
\www.microscopyU.com\tutorial
s\java\phasecontrast\phasespeci
mens\index.html
\primer\java\contrast\rounded\in
dex.html
Feb 7
Contrast: Special microscopy
techniques -manipulating the
light within the microscope.
phase contrast, darkfield,
Hoffman modulation
\primer\java\darkfield\cardioid\in
dex.html
The Phase M icroscope
Chapter 7,
also pp
190-195
\www.microscopyU.com\articles\
phasecontrast\phasemicroscopy.
html
Alignment:
\www.microscopyU.com\tutorial
s\java\phasecontrast\microscopea
lignment\index.html
Hoffman:\primer\techniques\hof
fmanindex.html
Lab 2
(Feb 1214)
Lab exercise on Phase Contrast
microscopy - room 348
Feb 12
DIC (Differential Interference
Contrast), Polarization
microscopy, Fluorescence
microscopy.
Polarization :
\primer\java\polarizedlight\filters
\index.html
\primer\techniques\polarized\pol
arizedhome.html
Chapter 8,
(Pol)
Chapter
10 (DIC)
DIC:
\primer\techniques\dic\dicovervi
ew.html
\primer\java\dic\lightpaths\index.
html
\primer\techniques\dic\dicintro.ht
ml
Comparison of Phase and DIC
\primer\techniques\dic\dicphasec
omparison.html
Fluorescence:
/primer/techniques/fluorescence/i
ntroduction.html
Feb 14
Fluorescence Microscopy 1
/primer/java/jablonski/index.htm
l
/primer/techniques/fluorescence/
excitation.html
Chapter
11
The microscope:
/primer/techniques/fluorescence/
reflectlightpaths.html
/primer/java/microscopy/fluoresc
ence/index.html
Lab 3
(Feb1921)
Lab exercise on Fluorescence
microscopy and DIC - room
348.
Feb 19
Fluorescence Microscopy 2
(Dyes)
Feb 21
TIRF, FRAP
Feb 26
Confocal microscopes 1
Chapter
11
pp 245261
/www.microscopyU.com/articles
/confocal/index.html
/Confocal/theory/index.html
Chapter
13
Basic Info:
http://www.physics.emory.edu/~
weeks/confocal
M insky Paper: Check
Blackboard
M ultiphoton
/primer/java/multiphoton/excitati
onbleaching/index.html
Lab 4
(Feb 2628))
More on Fluorescence
Microscopy
Feb 28
Confocal Microscopes II
Chapter
14
March 5
Superresolution I - STED
Chapter
15,
pp349353
Lab 5
(March 57))
Critical Focus, Image
characteristics
March 7
Exam 1
March 19
Capturing Images Photography
Lab 6
(March
19-21)
Capturing images.
Digital Imaging - capture,
spatial resolution, bit depth,
image histograms.
Brightness/contrast, file types.
March 21
Note that we will use an image
processing program in class for
parts of this section of the
course. W e will use ImageJ,
which will be installed on the
laptop computers. You should
also install the program at
home. Be aware of the changes
that will be mentioned during
class.
primer\photomicrography\index.
html
Chapter
17
Intro\primer\digitalimaging\digit
alimagebasics.html
Chapter
18
Sampling Frequency - spatial
resolution
\primer\java\digitalimaging\proc
essing\samplefrequency\index.ht
ml
\primer\java\digitalimaging\proc
essing\spatialresolution\index.ht
ml
Bit Depth
Lecture Notes
primer\java\digitalimaging\proce
ssing\bitdepth\index.html
The web site for ImageJ
is:http://rsb.info.nih.gov/ij/
Image Histograms
\primer\java\digitalimaging\proc
essing\histogramstretching\index
.html
March 26
Image manipulations 1.,.,LUTs,
pseudocolor, image math,
Background subtraction
Lab 7.
(March
26-28)
Image manipulation with
captured images.
\primer\java\digitalimaging\proc
essing\backgroundsubtraction\in
dex.html
\primer\digitalimaging\imagepro
cessingintro.html
March 28
Image manipulations 2.
Convolutions, unsharp mask,
Fourier analysis
Kernels
\primer\java\digitalimaging\proc
essing\convolutionkernels\index.
html
Fourier Transformation
\primer\java\digitalimaging\proc
essing\fouriertransform\index.ht
ml
April 2
More on Luts, Color
Lab 8
(April 24)
Demonstration of Confocal
Microscope
April 4
Image Manipulation 3
Deconvolution
April 9
Image manipulations 4. Time
lapse, Labels
Lab 9
(April 911)
Instruction on Confocal
Microscope - Start on Projects
April 11
Image Manipulation - 5
calibrations
April 16
Image M anipulations 6. Stacks,
3-D imaging., confocal
revisited
Lab 9
(April 1618)
W ork with confocal images
W ork on Projects
April 18
FRET -
\primer\digitalimaging\imagepro
cessingsteps.html
Lab Manual
298-304
pp235245
April 25
Colocalization -
Lab 10
(April 2325)
W ork on Projects
April 25
Quantitation of
Fluorescence-Quantitation of
Measurements
April 30
PALM , STORM Ñ
superresolution again
Open Lab
(30-May
2)
W ork on Projects
May 2
Exam 2
Open Lab
from Now
On..
W ork on Projects.
May 9
439-442
1-3+ Class presentations, Pizza
Party
pp 335343