Bi 227: Methods of Modern Microscopy
California Institute of Technology - Winter 2018
Andres Collazo
TA: Cai Tong Ng




Mon 10:00-11:00 am (Braun 152 was 151)
Wed 10:00-11:00 am (not every Wednesday, see schedule for room)
Lab: Church B168 (Phone Number x6094)



Student group list

Please contact Cai Tong



Syllabus (updated 3/5)

week 1
Introduction to Microscopes (Koehler illumination, Confocal microscopy)
01/03: Administrative details and Introductions (152 Braun)
(Assignment 1)
Training sessions to be scheduled with Cai Tong and Andres
Download LSM310 manual
Download LSM410 manual
Download LSM410 full manual
Manuals for BIF Microscopes (LARGE File)
(Lecture 01)

01/08: Hands on with the microscopes (B168 Church)

week 2
Applying Geometrical Optics (Making the Rochester Cloak)
01/08: Lecture on Geometrical optics and Rochester Cloak (152 Braun)
(Assignment 2)
(Lecture 02)

01/10: Building invisibility cloak with lenses (B168 Church)

week 3
3D Laser Scanning Confocal Microscopy (LSCM)
01/15: No class (Martin Luther King Day) Institute Holiday

01/17: Discuss assignments (152 Braun, 10:00 am)
(Assignment 3)
(Exciter power meter manual)

week 4
Begin Building a Light Sheet Microscope (
01/22: Light sheet fluorescence microscopy; Guest lecture by Dr. Alon Greenbaum (152 Braun) (Lecture 03)

01/24: Work on assignments (B168 Church)

week 5
Fluorescent Correlation Spectroscopy (FCS) vs FRAP 
01/29: FCS vs FRAP Lecture (152 Braun)
(Lecture 04) (Assignment 4) (FCS guide) (FRAP guide)

Afternoon lab meet in BIF (B133 Beckman Institute)

01/31: Final Project Proposal due!

week 6
Live Imaging Zebrafish embryos
02/05: Introduction to Zebrafish (152 Braun)
(Lecture 05) (Assignment 5)

02/07: Student presentations for Assignment 3 (152 Braun; 10:00 am)

week 7
Multispectral Imaging Lab
02/12: Multispectral Imaging; Guest Lecture by Steven Wilbert (152 Braun) (Lecture 06)

02/14: Meet in BIF (B133 Beckman Institute)

week 8
Work on Assignments and building light sheet
02/19: No class (President's Day) Institute Holiday

02/21: Work on light sheet (B168 Church)

week 9
Work on Assignments and building light sheet
02/26: Student presentations (10:00 AM, 152 Braun);
Afternoon, Work on light sheet (B168 Church)
(Light sheet instructions)

02/28: Work on light sheet (B168 Church)

week 10
Super-resolution Microscopy
03/05: Super-resolution microscopy lecture (152 Braun)
(Lecture 07)

03/07: Oral presentations for final project (10 am)

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

Cai Tong Ng, cng AT

By appointment as well.



Obtaining keys to Church 68

Please contact Cai Tong



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