Bi/BE 177: Principles of Modern Microscopy
California Institute of Technology - Winter 2019

Andres Collazo, Ph.D., preferred gender pronoun 'he'
TA: Ke (Keke) Ding, preferred gender pronoun 'he'
TA: Sandy Wong, preferred gender pronoun 'she'




  Tuesday and Thursday 10:30 am - 12:00 pm
Broad 200 Seminar Room



Lecture Schedule (updated 3/7)

Introduction and course review
(Lecture 01) No assignment. Feynman Lecture 26

Basic (Geometrical) Optics
(Lecture 02) Homework 1 (due beginning of class 1/17)
Reading 1, debate about negative refractive indices.
Will discuss reading on 1/17. Feynman Lecture 27.

Design and layout of real microscopes
(Lecture 03) Homework 2 (due beginning of class 1/22).

Diffraction and resolution
(Lecture 04) Homework 1 due. Diffraction App.
Discuss reading 1.

Illumination and detectors for imaging
(Lecture 05) Homework 2 due. Laser handout.

Wide field fluorescence microscopy
(Lecture 06) Homework 3 (due beginning of class 1/31).

Confocal microscopy: Adding the 3rd dimension
(Lecture 07) No assignment.

Contrast and resolution
(Lecture 08) No assignment. Homework 3 due.
Decide on and get approval for a paper for project 1.

Polarized Light Microscopy and Nomarski (DIC)
(Lecture 09) Homework 4 (due beginning of class 2/14).

Research applications of microscopy
(Lecture 10) Guest Lectures by Ke Ding, Dr. Brady Weissbourd and Sandy Wong.

Multispectral imaging
(Lecture 11) Guest lecture by Steven Wilbert, Graduate Student in BBE.

02/12: First Project Due during class.

Scattering and imaging: Clearing and adaptive optics
(Lecture 12) Homework 4 due.

Single molecule imaging: Fluorescence correlation spectroscopy & FRAP, FLIM
(Lecture 13) Reading 2, eLIFE paper on novel optics. Will discuss on 2/28. Homework 5 (due beginning of class 2/28).

Image processing
(Lecture 14) Guest lecture by Guest lecture by Dr. Alexandre Cunha, Director of the Center for Advanced Methods in Biological Image Analysis, CAMBIA.

FRET, TIRFM, Super-resolution microscopy I (NSOM)
(Lecture 15) Reading 4, the good the bad and the ugly. Will discuss on 3/07.

Super-resolution microscopy II (STED, PALM, SIM)
(Lecture 16) Homework 6 (due beginning of class 3/07). Homework 5 due. Will discuss Reading 2.

Light sheet fluorescence microscopy
(Lecture 17) Guest lecture by Dr. Thai Truong, Assistant Research Professor, Department of Molecular and Computational Biology, USC. Reading 3, OpenSpim review.

More fast imaging: SLM, holographic imaging
(Lecture 18) Will discuss Reading 4. Homework 6 due.

Electron microscopy
(Lecture 19) Guest lecture by Dr. Paul Webster.

03/15: Final Project Due



Office Hours

Andres Collazo, acollazo AT
Phone: x2761 or x2863
Friday 2-4 PM, 226 or B133 in the Beckman Institute

By appointment as well.

Ke Ding, dingke AT
Phone: x
By appointment

Sandy Wong, wwwong AT
Phone: x5840
By appointment



Reading Projects

  Read and study a published paper in a mainstream journal. Write a short report concerning this paper. The report should be ~5 pages long, double spaced. Get pre-approval of TA on paper/topic.

2nd Project will be either written or an oral presentation presented to the class.
Grading Criteria





6 Simple Problem sets
Paper reading project (2 per term)
No midterm or final exam




Grades based on the Homework and the Projects.
Homework, Project 1, Project 2 are given equal weight.
Late homework assignments are not accepted.
Score can be dropped with medical or Dean's excuse.



Course Description

Lectures and discussions on the underlying principles behind digital, video, differential interference contrast, phase contrast, confocal, and two-photon microscopy. The course will begin with basic geometric optics and characteristics of lenses and microscopes. Specific attention will be given to how different imaging elements such as filters, detectors, and objective lenses contribute to the final image. Course work will include critical evaluation of published images and design strategies for simple optical systems and the analysis and presentation of two- and three-dimensional images. The role of light microscopy in the history of science will be an underlying theme. No prior knowledge of microscopy will be assumed.



Auditors and non-traditional students

Auditors are welcome to take the Course, and, if they wish, they can do the homework problem sets and readings.




Bi177 & Bi227 website
Biological Imaging Facility
Microscope Primer
Zeiss Microscopy from the Very Beginning
Nikon Microscopy U
Olympus Microscopy Primer
Beckman Institute