Bi 227: Methods of Modern Microscopy
California Institute of Technology - Fall 2009
Scott E. Fraser and Willy Supatto
TA: Edward M. Perkins




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



Student group list

Preliminary list available here



Syllabus (updated 10/02)

week 1
10/02: Administrative session
Training sessions to be scheduled with Ned
Download LSM310 manual
Download LSM410 manual

week 2
10/05: Assignement #1
2D CLSM imaging of fixed samples
Download assigment #1

10/09: Q&A session + Introduction to lasers (John Choi)

week 3
10/12: Assignement #2
3D and multi-channel CLSM imaging of fixed samples
Download assigment #2

10/16: Student presentations (Assignement #1)

week 4
10/19: Assignement #3
Live imaging I: fly embryos
Download assigment #3

10/23: Student presentations (Assignement #2)

week 5
10/26: Assignement #4
Live imaging II: zebrafish embryos
Download assigment #4

10/30: Student presentations (Assignement #3)

week 6
11/02: Assignement #5
Image analysis
Download assigment #5
Download Sample Images for assigment #5
Final Project proposal due!

11/06: no class (Biology division retreat)

week 7
11/09: Feedback on final project proposal

11/13: Student presentations (Assignement #4)

week 8
11/16: Final project Q&A

11/20: Student presentations (Assignement #5)

week 9
11/23: Final project Q&A

11/27: no class (Thanksgiving)

week 10
11/30: Final project Q&A

12/04: Student presentations (Final project)




50% Weekly lab assignments
50% Final project
see the grading policy here
see the Final Project rules



Office Hours

By appointment:
Willy Supatto, supatto AT, x2863
Edward M. Perkins, ned AT



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 4 Calendars: (1) Bi227 CLASS 310, (2) Bi227 CLASS 410 (3) Bi227 CLASS 410 NLO, and (4) 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