
TuTh. 910AM
3109 Etcheverry Hall
3 Units
The course will be a detailed overview of the practice of light microscopy as applied to scientific investigation. The emphasis of the course will be on the use of the light microscope by biological scientists, however students of other disciplines are welcome. We will cover optical microscope theory, microscope components and mechanics, and all modern optical techniques from Brightfield through Deconvolution microscopy, Structured Illumination, and others. Instruction will consist of lectures, demonstrations, and practice using the light microscopes in the CNR Biological Imaging Facility and the GPBB Teaching facility.
Laboratory: The laboratory is in 209 GPBB, and will consist of one session per week. Each student is responsible for one laboratory session per week. Lab times are:Section 101 (CCN 70528): Thursday 25PM, 209 GPB
Section 102 (CCN 70531): Friday 25PM, 209 GPB
Grading: There will be a Midterm written exam and lab practical, plus a written Final Exam. For labs, students will be required to complete at least one worksheet for each of the labs. Worksheet is due at the end of that lab. In addition, a project is required for the class. It consists of a written paper. A description of the project will be given toward the middle of the semester.
Syllabus
|
Date
|
Lecture/Lab topic |
|
|
Lecture
|
Topic in Lecture |
Lab topic
|
|
Aug 25
|
Introduction, Light and Refraction |
No Lab
|
|
30
|
Microscope optics: Lenses, Imaging, and Resolution |
|
|
Sept 1
|
Lens aberrations (spherical, chromatic), The compound microscope , Microscope Standard Lengths |
Sample preparation (1,2)
|
|
6
|
The Condenser: history, optics & Köhler illumination |
Köhler illumination (8,9)
Focus Examples |
|
8
|
|
|
|
13
|
Contrast derived from Light Scattering: Darkfield microscopy, Rheinberg Illumination, Oblique Illumination |
Darkfield (15,16)
|
|
15
|
Eyepieces, Inverted Microscope, Stereo Microscope |
|
|
20
|
Polarized light microscopy I: Polarized light, Anisotropy, Types of birefringence, Polarized light microscope |
Polarized Light Microscopy (22,23)
|
|
22
|
Polarized light microscopy II, Generation of colors, Quantitative PLM |
|
|
27
|
PLM II |
Phase Contrast (29,30)
|
|
29
|
|
|
|
Oct 4
|
Interferometry, Differential Interference Contrast Presentation |
DIC (6,7)
|
|
6
|
|
|
|
11
|
Review of transmitted light techniques, Key to determining imaging method, Sample Exam Questions |
Lab Exam (Oct 13)
|
|
13
|
Midterm Exam |
Lab Exam (Oct 14)
|
|
18
|
|
|
|
20
|
Fluorescence (20,21)
|
|
|
25
|
Digital Imaging, Nyquist sampling, Digital imaging for microscopy, |
|
|
27
|
Confocal Microscopy I (28,29)
|
|
|
Nov 1
|
|
|
|
3
|
Confocal Microscopy II (3,4)
|
|
|
8
|
Deconvolution microscopy II, presentation |
|
|
10
|
No Lab (Holiday 10,11)
|
|
|
15
|
High Speed and Live-Cell imaging: Spinning Disk & Sweep Scanners, Nipkow disks, Slit scanning confocal microscopes |
Deconvolution (16,17)
|
|
17
|
|
|
|
22
|
No lab
|
|
|
24, 25
|
Holiday |
No Lab
|
|
29
|
Super Resolution: STED, PALM, Structured Illumination |
|
|
Dec 1
|
Historical Perspectives: The Golub Collection |
ALS tour (Dec 1)
Take the BLUE LBNL bus on Hearst by Tolman |
|
7
|
Final Review. Comparison of Advanced Fluorescence Techniques: BF Review, Fluor review, Advanced Review, |
ALS tour (Dec 2)
Take the BLUE LBNL bus on Hearst by Tolman |
|
9
|
No lecture. For you to use in preparation for the exam.
|
|
|
Dec 13,
36PM |
Final Exam |
|
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