Bi 227: Methods of Modern Microscopy
California Institute of Technology - Winter 2016
Andres Collazo
TA: Yonil Jung




Mon 10:00-11:00 am (Braun 151)
Wed 10:00-11:00 am (see schedule for room)
Lab: Church 68 (Phone Number x6094)



Student group list

Please contact Yon



Syllabus (updated 12/30)

week 1
Introduction to Microscopes (Koehler illumination, Confocal microscopy)
01/04: Administrative details and Introductions (151 Braun)
(Assignment 1)
Training sessions to be scheduled with Yon and Andres
Download LSM310 manual
Download LSM410 manual
Download LSM410 full manual
Manuals for BIF Microscopes
(Lecture 01)

01/06: Hands on with the microscopes (68 Church)

week 2
Applying Geometrical Optics (Making the Rochester Cloak)
01/11: Lecture on Geometrical optics and Rochester Cloak (151 Braun)
(Assignment 2)
(Lecture 02)

01/13: Building invisibility cloak with lenses (68 Church)

week 3
2D Laser Scanning Confocal Microscopy (LSCM)
01/18: No class (Martin Luther King Day) Institute Holiday

01/20: Discuss assignments (68 Church)
(Assignment 3)
(Exciter manual)

week 4
3D LSCM; Begin Building a Light Sheet Microscope (
01/25: Light sheet fluorescence microscopy lecture by Dr. Antti Lignell (151 Braun) (Lecture 03)

01/27: Work on assignments (68 Church)

week 5
Live Imaging I: Drosophila embryos
02/01: Introduction to Drosophila (Yonil Jung, guest lecture) (151 Braun) (Lecture 04) (Assignment 4)

02/03: Final Project Proposal due!

week 6
Live Imaging II: Zebrafish embryos
02/08: Introduction to Zebrafish (151 Braun)
(Lecture 05) (Assignment 5)

02/10: Student presentations for Assignment 3 (60 Church)

week 7
Multispectral Imaging Lab
02/15: No class (President?s Day) Institute Holiday

02/17: Meet in BIF (B133 Beckman Institute)

week 8
Fluorescent Correlation Spectroscopy (FCS)
02/22: FCS Lecture (151 Braun)
(Lecture 06)

02/24: Meet in BIF (B133 Beckman Institute)

02/25: Eric Betzig talk on Super Resolution Microscopy
Physics Research Conference at 4:00 P.M. in 201 E. Bridge

week 9
Comparisons of Different Confocals & Light Sheet
02/29: Work on project and this week?s topic

03/02: Discussion on this week's topic

week 10
Multispectral Imaging Lecture
03/07: Multispectral Imaging lecture (151 Braun)
(Lecture 07)

03/09: Work on project and this week?s topic

03/16: Final Project Due




50% Lab assignments
50% Final project
Download Final Project Instructions



Office Hours

Andres Collazo, acollazo AT
Phone: x2761 or x2863
Friday 2-4 PM, 226 or B133 in the Beckman Institute

Yonil Jung, jung830307 AT

By appointment as well.



Obtaining keys to Church 68

Please contact Yon



Microscope Calendar Access

Students need to access the calendar system for microscope reservations:
- go to:
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