Bi277 Methods in Modern Microscopy, Fall 2007–08

Michael Liebling, Scott E. Fraser
TA: Louisa Liberman
California Institute of Technology

Mon 3–4pm Church 68 (phone: x6094)
Fri 2–4pm Church 60


Week 1 October 1 Administrative Session
Room keys, class program, attendance (Bi177 and Bi227), grading, general microscope rules, signup calendars, students choose groups.
Download Syllabus (pdf, 48kB)
October 5 No class
Week 2 October 8 Widefield Microscopy
Topics: Brightfield (Köhler illumination), polarization, and epi-fluorescence microscopy
Samples: fixed slides
Download Assignment #1: (pdf, 20kB)
October 12 Q+A Widefield Microscopy
Week 3 October 15 Confocal Laser Scanning Microscopy (LSM) Training, Groups I-IV (Chris Waters)
(Hand out LSM 310 and LSM 410 documentation)
Samples: fixed slides
October 19 LSM Training, Groups V-VIII (Chris Waters)
(Hand out LSM 310 and LSM 410 documentation)
Samples: fixed slides
Download 310 Manual (pdf, 528kB)
Download 410 Manual (pdf, 544kB)
Week 4 October 22 LSM Thin Fixed Samples
Goal: effects on image quality of laser intensity, integration time, pinhole aperture; bleaching Samples: fixed pollen, stem, mold, and cell slides, fluorescent microbeads
Download Assignment #2: (pdf, 120kB)
October 26 No class (Biology Retreat)
Week 5 October 29 LSM Live Thin Samples
Goal: controlled imaging environment, phototoxicity, time-series, multiple-channel imaging
Samples: C.elegans
Download Assignment #3: (pdf, 112kB)
November 2 Student Presentations 1 (Thin Fixed Samples)
Week 6 November 5 LSM Thick Fixed Samples
Dissecting Microscopes (and Fluorescence Stereo-Microscope) Goal: sample mounting
Sample: zebrafish embryos
<--> Goal: 3D imaging and visualization of fixed samples
Samples: fixed pollen, stem, mold and cell slides, fluorescent microbeads
Download Assignment #4: (pdf, 104kB)
November 9 Student Presentations 2 (Live Thin Samples)
Week 7 November 12 Bi 177 (1:00-2:30 BBB24): Resolution, Detectability & Motion
November 12 Zebrafish Timelapse Imaging for Cell Tracking
Goal: In vivo timelapse imaging, working distance
Samples: Bodipy TR dyed zebrafish embryos
Download Assignment #5: (pdf, 532kB)
November 14 Bi 177 (1:00-2:30 BBB24): 3D Reconstruction & Rendering
November 16 Student Presentations 3 (Thick Fixed Samples)
Week 8 November 19(3-4pm) Image Analysis I: Introduction to Visualization and Tracking with Imaris
Data: Zebrafish timelapses
November 23 No class (Thanksgiving)
Week 9 November 26 Drosophila Timelapse Imaging
Download Assignment #6: (pdf, 200kB)
November 30 Student Presentations 4 (Zebrafish Cell Tracking and Visualization)
Week 10 December 3 Image Analysis II: Quantitative Analysis with Imaris
Data: data acquired during the class
December 7 Student Presentations 5 (Drosophila Imaging and Cell Tracking)
Week 11 December 14, 4pm: Final paper is due.
Download instructions for final paper: (pdf, 124kB)

    50% Lab work
    50% Final paper (Download instructions (pdf, 124kB))

Office Hours 
By appointment.
    Scott Fraser, sefraser AT
    Michael Liebling, liebling AT, x2863
    Louisa Liberman, louisa AT, x5952

Obtaining Keys to Church 68 
    Mary Marsh
    105 Kerckhoff
    marshm AT

Microscope Calendar Access 
Important: Mac Users, the calendar system will not register you properly if you use Safari as your browser. If you have problems registering, use Firefox.
Students need to access the calendar system for microscope reservations:
    - go to:
    - click on "If you are not yet a registered user of the calendar, please click here."
    - fill in required information
    - Request access to 2 Calendars:
        (1) 310
        (2) 410teaching

This will send an email to request official access to the calendars.

Notes about Scope Calendar Reservations and usage:
    - Never use the microscopes 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 and then send email to: bi227 AT to notify others of open time slot
    -Try to avoid imaging late at night, since no one will be around to help if you have a problem.

Signup Calendar for 310 and 410 Scopes
Bi177 website
Imaris (Bitplane AG)
Bitplane Training Center
Microscopy Primer
Microscopy from the Beginning (Zeiss)

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