Bi 227: Methods of Modern Microscopy
California Institute of Technology - Fall 2008
John Choi and Willy Supatto
TA: Louisa Liberman


Mon 3:00-4:00 pm (Chrurch 68)
Fri 2:00-4:00 pm (Chrurch 60)
Lab: Church 68


Student group list
available here


Syllabus (updated 10/23)
week 1
09/29: Administrative session
Training sessions to be scheduled with Chris Waters
Download LSM310 manual
Download LSM410 manual
10/03: Imaris Seminar/training
week 2
10/06: Assignement #1
2D Imaging of fixed samples: widefield and CLSM microscopy
10/10: Q&A session
week 3
10/13: Assignement #2
3D and multi-channel CLSM imaging of fixed samples
10/17: Student presentations (Assignement #1)
week 4
10/20: Assignement #3
Live imaging I: fly embryos
10/24: Student presentations (Assignement #2)
week 5
10/27: Assignement #4
Live imaging II: zebrafish embryos
10/31: Student presentations (Assignement #3)
week 6
11/03: Assignement #5
Image analysis
> Download the Sample Images (zip file)
11/07: Student presentations (Assignement #4)
week 7
11/10: Assignement #6
FRAP experiment
Final Project proposal due!
11/14: Student presentations (Assignement #5)
week 8
11/17: Final project Q&A
11/21: Student presentations (Assignement #6)
week 9
11/24: Final project Q&A
11/28: no class (Thanksgiving)
week 10
12/01: Final project Q&A
12/05: Student presentations (Final project)


60% Weekly lab assignments
40% Final project
see the grading policy here
see the Final Project rules here


Office Hours
By appointment:
John Choi, johnchoi AT, x4499
Willy Supatto, supatto AT, x2863
Louisa Liberman, louisa AT, x5952


Obtaining keys to Church 68
Contact: Mary Marsh, 110 Kerckhoff, marshm AT, x6444


Microscope Calendar Access
Students need to access the calendar system for microscope and Imaris station reservations:
- go to:
- click on "New users please Register here".
- fill in required information.
- use "Caltech Labs" as affiliation
- Request access to 3 Calendars: (1) Bi227 310 (2) Bi227 410 and (3) Bi 227 IMARIS.
This will send an email to request official access to the calendars.
Notes about Scope Calendar reservations and usage:
- Never use the microscopes or the Imaris station without reserving it first
- Be considerate of others
- reserve reasonable amounts of time
- If you cannot make it to your reserved time please delete your reservation on calendar.
- Try to avoid imaging late at night, since no one will be around to help if you have a problem.


Bi177 & Bi227 website
Imaris (Bitplane AG)
Bitplane Training Center
Microscope Primer
Microscopy from the Very Beginning (Zeiss)
Olympus Microscopy Primer