Bi 177: Principles of Modern Microscopy
California Institute of Technology - Fall 2010
Prof. Scott E Fraser
TAs: Danielle Bower, dvbrown AT,
Jessica Ricci, jricci AT


Mon, Wed, Fri 1:00-2:15 pm
Broad 100 Lecture Hall


Lecture schedule (MAY BE UPDATED!)
Oct 06
Lecture 01: Basic optics
Homework 1, Due 10/8/10 (beginning of class)
Oct 08
Lecture 02: Design and layout of real microscopes
Homework 2, Due 10/11/10
Oct 11
Lecture 03: Wide Field Fluorescence Microscopy
Oct 13
Lecture 04: Lasers (physics, types, functions)
Oct 15
Lecture 05: Widefield vs laser scanning microscopy: adding the 3rd dimension
Homework 3, Due 10/20/10
Oct 18
Lecture 06: Practical considerations in a confocal microscope

** By 1pm email TAs the paper you will review for project 1
Oct 20
Lecture 07: Techniques for enhancing intrinsic contrast

** TAs will approve your paper selection or request a new one
Oct 22
Lecture 08: Resolution, contrast, and detection
Nov 01
Lecture 09: Multiple labeling and multi-spectral imaging

** Draft of project 1 paper due at the beginning of class! Exchange with peers to review.
Nov 03
Lecture 10: FRET

**Comments on your peer's paper due at beginning of class!
Nov 05
Lecture 11: Quantitative Fluorescence Microscopy
Nov 08
Lecture 12: Fast fluorescence and lightsheet microscopy

**Final revised project 1 paper due at beginning of class!
Nov 10
Lecture 13: Electron microscopy and tomography (Grant Jensen)

**By 1pm email us the paper you will review for project 2.
Nov 15
Eric Betzig's seminar on super-resolution microscopy
Nov 17
Lecture 14: MRI and MR microscopy (Russ Jacobs)
Nov 19
Lecture 15: Emerging imaging techniques I (NSOM, SIM, AFM, OPT, OCT)

** Draft of project 2 paper due at the beginning of class. Exchange for peer review.
Nov 22
Lecture 16: Emerging imaging techniques II (STED, 4pi, PALM/STORM)
Nov 24
**Complete peer review and exchange comments.

Dec 03
**Final, revised project 2 due by 1pm!
Please turn in to Danielle (Brown OR Bower)'s mailbox in the BI lobby:
1) your first draft of paper #2,
2) the peer comments you received, and
3) your final draft,
all paper-clipped together.



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