Techniques in Light Microscopy – The Biological Imaging Facility

The BIF offers a UCB lecture & lab course, PMB185, that covers all aspects of Light Microscopy. These are the topics covered.

PMB 185 Techniques in Light Microscopy

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, labs, and Demonstrations.

Grading: There is a Midterm written exam, Midterm Practical exam, and Final written Exam. For labs, students are required to complete 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 describing your forensic analysis of an unknown substance.

The textbook is Techniques in Light Microscopy. It is available for $26 at Instant Copying and Laser Printing (2138 University Ave, Berkeley).

Lecture	Topic in Lecture	Reading pages	Lab topic (Fridays)
Aug 25	Introduction
27	Light and Refraction	10–15	No Lab
30	Microscope Optics: Lenses and Conjugate planes	16–18
Sept 1	Microscope optics: Imaging and Resolution	18–21
3	Numerical Aperture and Resolution	22–25	1: Microscope optics
6	No Class
8	Lens aberrations (spherical, chromatic)	26–32
10	Microscope configurations: The compound microscope, Microscope Standard Lengths	33–37	2: Köhler illumination Focus Examples
13	The Condenser: history, optics & Köhler illumination	38–42
15	Objectives, objective designations, Eyepieces	43–52
17	Darkfield microscopy, Rheinberg Illumination, Oblique Illumination	54–58	3: Darkfield
20	Polarized light, Anisotropy, Types of birefringence, Polarized light microscope	59–71
22	Polarized light microscopy, Generation of colors,	72–76
24	Polarized light microscopy: Quantitative PLM	77–80	4: Polarized Light Microscopy
27	Phase Contrast microscopy I	81–82
29	Phase Contrast microscopy II	83–88
Oct 1	Inverted Microscope, Stereo Microscope,	53	5: Phase Contrast
4	Interferometry, Differential Interference Contrast Presentation; DIC microscope	89–98
6	PlasDIC	99–100
8	Hoffman Modulation Contrast	100–102	6: DIC
11	Review of transmitted light techniques, Key to determining imaging method	103–105
13	Microscope Jeopardy
15	Midterm Exam		7: Lab Practical Exam
18	Fluorescence Microscopy, Stokes Shift, Types of sample fluorescence	106–110
20	Fluorescence Microscope	110–115
22	Digital Imaging, Nyquist sampling, Digital imaging for microscopy	131–135	8: Epifluorescence microscopy
25	Laser scanning confocal microscopy I, presentation	123–130
27	Laser scanning confocal microscopy II, resolution	ditto
29	Laser scanning confocal microscopy III	ditto	9: Fluorescence Probing
Nov 1	Spinning Disk & Sweep Scanners, Nipkow disks	136–140
3	Two photon microscopy and resolution, presentation	141–146
5	Two photon microscopy II	146–148	10: Confocal microscopy (Zoom Lecture)
8	Restoration microscopy I, Basis, PSF, Methods,	157–166
10	Restoration Microscopy II	ditto
12	SPIM — Light Sheet Imaging	149–156	11: Project Explained
15	Super Resolution: Structured Illumination Microscopy (SIM)	167–173
17	Super Resolution: STED	174–182
19	Super Resolution: PALM/StORM	183–187	12: SIM (Zoom Lecture)
22	Advanced fluorescence imaging: FRAP, FRET, FLIM	117–119
24	Holiday: No Class
26	Holiday: No Class		Holiday: No Lab
29	Total Internal Reflection microscopy, TIRF microscope, Implications;	119–121
Dec 1	Finals Review Resources, History of the Microscope
3	Question & Answer session	188–198	13: Tour of the Golub Collection
6	RRR Week: No Lecture
8	RRR Week: No Lecture.
10	RRR Week: No Lecture. Project Due 5PM. Upload to bCourses
13–16	The final exam will be Take-Home