Caltech - Bi177 - Fall 2009

Bi 177: Principles of Modern Microscopy

California Institute of Technology - Fall 2009

Prof. Scott E Fraser (SF)

Lecturers: Grant Jensen (GJ), John Choi (JC), Russ Jacobs (RJ), and Willy Supatto (WS)

TA: Judith Su, judy AT caltech.edu, x4499
Mailing list: bi177students AT caltech.edu

Hours

Mon and Wed 1:00-2:30 pm

Broad 100 Lecture Hall

Lecture schedule (updated 10/25/09)

Sep 30

Lecture 00: Introduction to Course (WS)
Syllabus

Oct 05

Lecture 01: Basic optics (SF)
Homework 1, Due 10/7/09

Oct 07

Lecture 02: Design and layout of real microscopes (SF)
Homework 2, Due 10/12/09 (beginning of class)

Oct 12

Lecture 03: Wide Field Fluorescence Microscopy (JC, johnchoi AT caltech.edu)
Homework 3, Due 10/14/09 (beginning of class)

Oct 14

Lecture 04: Lasers (physics, types, functions) (JC)
Homework 4, Due 10/28/09 (beginning of class)
** Get paper choice approved by TA

Oct 19

Lecture 05: Widefield vs laser scanning microscopy: adding the 3rd dimension (SF)
Homework 5, Due 10/21/09 (beginning of class)
** Exchange drafts for peer review

Oct 21

Lecture 06: Enhancing intrinsic contrast (SF)

** Return peer review draft

Oct 26

Lecture 07: Contrast, resolution, and AVEC (SF)

Oct 28

Lecture 08: Volume imaging (JC)

Nov 02

Lecture 09: Multiphoton microscopy (2PEF, SHG, THG, CARS) (WS)

** Project 1 due at the beginning of class!

Nov 04

Lecture 10: Motion and Fast Imaging (WS)

Nov 09

Lecture 11: Multiple labeling and multispectral imaging (SF)

Nov 11

Lecture 12: Quantitative fluorescence microscopy (FLIM, FRET, FRAP, FCS) (WS)

Nov 16

Lecture 13: Digital images: formation, visualization, processing, and analysis (WS)

Nov 18

Lecture 14: Electron microscopy and tomography (GJ)

Nov 23

Lecture 15: MRI and MR microscopy (RJ)

Nov 25

Meet with TA to discuss and approve project 2 (JS)

Nov 30

Lecture 16: Emerging imaging techniques I (NSOM and OCT) (SF)
** Exchange drafts for peer review

Dec 02

Lecture 17: Emerging imaging techniques II: far-field fluorescence nanoscopy (STED, nonlinear SIM, STORM/PALM) (WS)

** Return peer review draft
** Project 2 Due Dec 6th (TA mailbox, first floor of BI). Will collect by 1pm Monday, Dec 7th.

Reading Projects

Read and study a published paper in a mainstream journal. Write a short report concerning this paper. The report should be ~5 pages long. Get pre-approval of TA on paper/topic.

Peer Review Form
Grading Criteria

Coursework

Reading

6 Simple problem sets

Paper reading project (2 per term)

No midterm or final exam

Grading

Grades based on the Homework and the Projects.

Homework, Project 1, Project 2 are given equal weight.

Late homework assignments are not accepted.

Score can be dropped with medical or Dean's excuse.

Auditors and non-traditional students

Auditors are welcome to take the Course, but are required to do the homework problem sets and reading.

Links

Bi177 & Bi227 website

Microscope Primer

Microscopy from the Very Beginning (Zeiss)

Olympus Microscopy Primer



			Bi 177: Principles of Modern Microscopy California Institute of Technology - Fall 2009 Prof. Scott E Fraser (SF) Lecturers: Grant Jensen (GJ), John Choi (JC), Russ Jacobs (RJ), and Willy Supatto (WS) TA: Judith Su, judy AT caltech.edu, x4499 Mailing list: bi177students AT caltech.edu


			Hours

			Mon and Wed 1:00-2:30 pm Broad 100 Lecture Hall

			Lecture schedule (updated 10/25/09)

	Sep 30		Lecture 00: Introduction to Course (WS) Syllabus

	Oct 05		Lecture 01: Basic optics (SF) Homework 1, Due 10/7/09

	Oct 07		Lecture 02: Design and layout of real microscopes (SF) Homework 2, Due 10/12/09 (beginning of class)

	Oct 12		Lecture 03: Wide Field Fluorescence Microscopy (JC, johnchoi AT caltech.edu) Homework 3, Due 10/14/09 (beginning of class)

	Oct 14		Lecture 04: Lasers (physics, types, functions) (JC) Homework 4, Due 10/28/09 (beginning of class) ** Get paper choice approved by TA

	Oct 19		Lecture 05: Widefield vs laser scanning microscopy: adding the 3rd dimension (SF) Homework 5, Due 10/21/09 (beginning of class) ** Exchange drafts for peer review

	Oct 21		Lecture 06: Enhancing intrinsic contrast (SF) ** Return peer review draft

	Oct 26		Lecture 07: Contrast, resolution, and AVEC (SF)

	Oct 28		Lecture 08: Volume imaging (JC)

	Nov 02		Lecture 09: Multiphoton microscopy (2PEF, SHG, THG, CARS) (WS) ** Project 1 due at the beginning of class!

	Nov 04		Lecture 10: Motion and Fast Imaging (WS)

	Nov 09		Lecture 11: Multiple labeling and multispectral imaging (SF)

	Nov 11		Lecture 12: Quantitative fluorescence microscopy (FLIM, FRET, FRAP, FCS) (WS)

	Nov 16		Lecture 13: Digital images: formation, visualization, processing, and analysis (WS)

	Nov 18		Lecture 14: Electron microscopy and tomography (GJ)

	Nov 23		Lecture 15: MRI and MR microscopy (RJ)

	Nov 25		Meet with TA to discuss and approve project 2 (JS)

	Nov 30		Lecture 16: Emerging imaging techniques I (NSOM and OCT) (SF) ** Exchange drafts for peer review

	Dec 02		Lecture 17: Emerging imaging techniques II: far-field fluorescence nanoscopy (STED, nonlinear SIM, STORM/PALM) (WS) Return peer review draft Project 2 Due Dec 6th (TA mailbox, first floor of BI). Will collect by 1pm Monday, Dec 7th.

			Reading Projects

			Read and study a published paper in a mainstream journal. Write a short report concerning this paper. The report should be ~5 pages long. Get pre-approval of TA on paper/topic. Peer Review Form Grading Criteria

			Coursework

			Reading 6 Simple problem sets Paper reading project (2 per term) No midterm or final exam

			Grading

			Grades based on the Homework and the Projects. Homework, Project 1, Project 2 are given equal weight. Late homework assignments are not accepted. Score can be dropped with medical or Dean's excuse.

			Auditors and non-traditional students

			Auditors are welcome to take the Course, but are required to do the homework problem sets and reading.

			Links

			Bi177 & Bi227 website Microscope Primer Microscopy from the Very Beginning (Zeiss) Olympus Microscopy Primer