Bi277 Methods in Modern Microscopy, Fall 2007–08
Michael Liebling, Scott E. Fraser
TA: Louisa Liberman
California Institute of Technology
Hours
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) |
Grading
50% Lab work
50% Final paper (Download instructions (pdf, 124kB))
Office Hours
By appointment.
Scott Fraser, sefraser AT caltech.edu
Michael Liebling, liebling AT caltech.edu, x2863
Louisa Liberman, louisa AT caltech.edu, x5952
Obtaining Keys to Church 68
Contact:
Mary Marsh
105 Kerckhoff
x6444
marshm AT its.caltech.edu
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: http://quad.bic.caltech.edu/
- 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 quad.bic.caltech.edu 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.
Links
Signup Calendar for 310 and 410 Scopes
Bi177 website
Imaris (Bitplane AG)
Bitplane Training Center
Microscopy Primer
Microscopy from the Beginning (Zeiss)
ImageJ