Bi 227: Methods of Modern Microscopy
California Institute of Technology - Winter 2020
Andres Collazo, Ph.D., preferred gender pronoun 'he, him'
TA: Steven Wilbert, preferred gender pronoun 'he, him'




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 Steven Wilbert



Syllabus (updated 2/18)

week 1
Introduction to Microscopes (Koehler illumination, Confocal microscopy)
01/06: Administrative details and Introductions (152 Braun)
(Assignment 1)
Training sessions to be scheduled with Steven and Andres
Download LSM310 manual
Download LSM410 manual
Download LSM410 full manual
Manuals for BIF Microscopes (LARGE File)
(Lecture 01)

01/08: Fiji Intro by Steven Wilbert; bring your laptops (10 am, 101 Kerckhoff)
Lab Time: Hands on with microscopes (B168 Church)

week 2
3D Laser Scanning Confocal Microscopy (LSCM)
01/13: Lecture on Confocal Microscopes (152 Braun)
(Assignment 2) (Lecture 02)

01/15: Students present Assignment 1 (10 am, 101 Kerckhoff)
Lab Time: Collect 3D confocal data sets (B168 Church)

week 3
Begin Building a Light Sheet Microscope (
01/20: No class (Martin Luther King Day) Institute Holiday

01/22:  Light sheet fluorescence microscopy; Guest lecture by Dr. Thai Truong (10 am, 101 Kerckhoff) (Lecture 03) 
Lab Time: Begin building light sheet microscope (B168 Church)
(Assignment 3) (OpenSPIM paper)

week 4
Live Imaging Zebrafish Embryos
01/27: Introduction to zebrafish lecture (152 Braun)
(Lecture 04)

01/29: Students present Assignment 2 (10 am, 101 Kerckhoff)
Lab Time: Set up zebrafish embryo timelapse; Demo Zeiss Z1 light sheet setup (B133 Beckman Institute)

week 5
Fluorescent Correlation Spectroscopy (FCS) vs FRAP 
02/03: FCS vs FRAP Lecture (152 Braun)
(Lecture 05) (Assignment 4) (FCS guide) (FRAP guide)

02/05: Lab Time: Collect FCS and FRAP data sets. Afternoon lab meet in BIF (B133 Beckman Institute)
Final Project Proposal due!

week 6
Multispectral Imaging Lab 
02/10: Multispectral Imaging; Lecture by Steven Wilbert (152 Braun)
(Lecture 06)

02/12: Lab Time: Spectral imaging of microbial biofilms

week 7
Super-resolution Microscopy 
02/17: No class (President's Day) Institute Holiday

02/19:  Super-resolution microscopy lecture (10 am, 101 Kerckhoff)
(Lecture 07) (Assignment 5)
Lab Time: Compare Airyscan to deconvolution (B133 Beckman Institute)

week 8
Work on Assignments and building light sheet
02/24: Fiji - Basic Image Analysis Lecture by Steven (152 Braun) (Lecture 08)

02/26: Students present Assignment 4 (10 am, 101 Kerckhoff)
Lab Time: Work on assignments and building light sheet

week 9
Work on Assignments and building light sheet
03/02: No lecture. Afternoon, Work on light sheet
(B168 Church)
(Light sheet instructions)

03/05: Students present Assignment 5 (10 am, 101 Kerckhoff)

week 10
Student Presentations of final project
03/09: Oral presentations for final project (152 Braun)

03/11: Oral presentations for final project (10 am, 101 Kerckhoff); Assignment 3 due.

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

Steven Wilbert, swilbert AT

By appointment as well.



Obtaining code for key to B168 Church

Please contact Steven Wilbert



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