Bi 177: Principles of Modern Microscopy
California Institute of Technology - Fall 2008
John Choi and Willy Supatto
TA: Judith Su


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


Lecture schedule (updated 10/12)
Sept 29
Lecture 01: Basic optics (JC)
>download homework (due Oct 01)
Oct 01
Lecture 02: Optics of real microscopes (JC)
>download homework (due Oct 13)
note: Imaris software presentation on Oct 03 (2-3pm in Broad 100)
Oct 06
Science Writing Workshop with Steven Youra (Project 1)
Oct 08
Science Writing Workshop with TA (Project 1)
Oct 13
Lecture 03: Widefield light microscopy (JC)
>download homework (due Oct 22)
Oct 15
Lecture 04: Contrast techniques (JC)
Oct 20
Lecture 05: Fluorescent microscopy (JC)
Oct 22
Lecture 06: Electron Microscopy and Tomography (Grant Jensen)
>download homework (due Oct 31)
Oct 27
Lecture 07: Confocal microscopy I (JC)
Oct 29
Lecture 08: Confocal microscopy II (JC)
>download the reading
Nov 03
Lecture 09: Multiphoton microscopy I (2PEF) (WS)
Nov 05
Lecture 10: Multiphoton microscopy II (SHG, THG, CARS) (WS)
Nov 10
Science Writing Workshop with TA (Project 2)
Nov 12
Lecture 11: MRI and MR microscopy (Russ Jacobs)
Nov 17
Lecture 12: Motion and fast imaging (WS)
Nov 19
Lecture 13: Labeling and multi-spectral imaging (WS)
Nov 24
Lecture 14: Quantitative fluorescence microscopy (FLIM, FRET, FRAP, FCS) (WS)
Nov 26
Lecture 15: Digital imaging I: image formation, visualization and processing (WS)
Dec 01
Lecture 16: Digital imaging II: 3D-reconstruction, image restoration and analysis (WS)
Dec 03
Lecture 17: Fluorescence nanoscopy (NSOM, TIRF, 4Pi, STED, nonlinear SIM, STORM-PALM-FPALM) (WS)


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.
>download the Reading Project Grading Criteria


Assignment Schedule (updated 10/12)
Reading Project 1:
Oct 06
Look for journal article (due Oct 13)
Oct 13
Write draft (due Oct 20*)
Oct 20
Do peer-review (due Oct 27*)
>download the Peer-Review Comment Sheet
Oct 27
Write final version of paper (due Oct 31)
Reading Project 2:
Nov 10
Look for journal article (due Nov 17)
Nov 17
Write draft (due Nov 24*)
Nov 24
Do peer-review (due Dec 01*)
Dec 01
Write final version of paper (due Dec 05**)
*due at beginning of class
** in TA mailbox


Course Work
Simple problem sets
Paper reading project (2 per term)
No mid-term of final exam


Grades based on the Homework and the Projects.
Homework, Project 1, Project 2 are given equal weight.
Late homework assignements 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