Bi 177: Principles of Modern Microscopy
California Institute of Technology - Fall 2009
Prof. Scott E Fraser (SF)
Lecturers: Grant Jensen (GJ), John Choi (JC), Russ Jacobs (RJ), and Willy Supatto (WS)
TA: Judith Su, judy AT, x4499
Mailing list: bi177students AT


Mon and Wed 1:00-2:30 pm
Broad 100 Lecture Hall


Lecture schedule (updated 10/25/09)
Sep 30
Lecture 00: Introduction to Course (WS)
Oct 05
Lecture 01: Basic optics (SF)
Homework 1, Due 10/7/09
Oct 07
Lecture 02: Design and layout of real microscopes (SF)
Homework 2, Due 10/12/09 (beginning of class)
Oct 12
Lecture 03: Wide Field Fluorescence Microscopy (JC, johnchoi AT
Homework 3, Due 10/14/09 (beginning of class)
Oct 14
Lecture 04: Lasers (physics, types, functions) (JC)
Homework 4, Due 10/28/09 (beginning of class)
** Get paper choice approved by TA
Oct 19
Lecture 05: Widefield vs laser scanning microscopy: adding the 3rd dimension (SF)
Homework 5, Due 10/21/09 (beginning of class)
** Exchange drafts for peer review
Oct 21
Lecture 06: Enhancing intrinsic contrast (SF)

** Return peer review draft
Oct 26
Lecture 07: Contrast, resolution, and AVEC (SF)
Oct 28
Lecture 08: Volume imaging (JC)
Nov 02
Lecture 09: Multiphoton microscopy (2PEF, SHG, THG, CARS) (WS)

** Project 1 due at the beginning of class!
Nov 04
Lecture 10: Motion and Fast Imaging (WS)
Nov 09
Lecture 11: Multiple labeling and multispectral imaging (SF)
Nov 11
Lecture 12: Quantitative fluorescence microscopy (FLIM, FRET, FRAP, FCS) (WS)
Nov 16
Lecture 13: Digital images: formation, visualization, processing, and analysis (WS)
Nov 18
Lecture 14: Electron microscopy and tomography (GJ)
Nov 23
Lecture 15: MRI and MR microscopy (RJ)
Nov 25
Meet with TA to discuss and approve project 2 (JS)
Nov 30
Lecture 16: Emerging imaging techniques I (NSOM and OCT) (SF)
** Exchange drafts for peer review
Dec 02
Lecture 17: Emerging imaging techniques II: far-field fluorescence nanoscopy (STED, nonlinear SIM, STORM/PALM) (WS)

** Return peer review draft
** Project 2 Due Dec 6th (TA mailbox, first floor of BI). Will collect by 1pm Monday, Dec 7th.



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. Get pre-approval of TA on paper/topic.

Peer Review Form
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.


Auditors and non-traditional students
Auditors are welcome to take the Course, but are required to do the homework problem sets and reading.


Bi177 & Bi227 website
Microscope Primer
Microscopy from the Very Beginning (Zeiss)
Olympus Microscopy Primer