First Reading: Two-photon microscopy

In the first meeting (Wednesday, September 30), after going over a few admininstrative matters we will talk about the following:

1) How to find biomedical optics papers online? For those of you planning to give a presentation and/or write a research article, this will be useful.

2) How to read a paper? As an example, we will examine this paper on 2 photon microscopy. Read as much of it as you can, and don't be afraid to skip confusing sections. We'll talk about the basic idea and the key things to look for in a paper.

We'll probably continue the discussion of this paper in the following week.

Things to keep in mind as you read the paper:
1) It's often productive to start with the diagrams.
2) Don't be afraid to skip stuff that you don't understand.
3) This is a review article, which means that it provides an overview of the field rather than discussing a specific experiment. Review articles tend to start out general and become more specialized. Don't be afraid if you find the later parts harder. (However, if you're a biologist, the last couple pages might be more interesting, while physicists and engineers will find the first few pages interesting.)
4) Another good introduction to this topic is at MicroscopyU. MicroscopyU is full of good stuff, and you should always consult it when you are reading an article and run across things that you don't understand.
5) In the first few pages of the paper, especially in box 2, you'll run across a "point spread function." MicroscopyU has an OK explanation of it. Here's another OK explanation. The Wikipedia article is horrible. We'll talk about this concept in class.

The basic idea of fluorescence microscopy is simple: You illuminate an object, and wherever it's illuminated it produces light. You'd like it if most of the light you detect comes from wherever the lens focuses the light, but sometimes (especially in tissue that scatters or distorts light) this isn't possible. Basically, light has to travel through other tissue to reach the focal spot, so the other stuff produces light too.

Two-photon microscopy gets around this by using a trick: For special dyes, the amount of light they produce is not proportional to the amount of light they get. Rather, it's proportional to the square of the amount of light it gets. (What this has to do with two photons will be explained in class.) So there's only a strong signal from the spot where the light is focused, and you detect that.

Anyway, we'll probably spend a week and a half reading this, because it introduces lots of important ideas related to imaging. Then we'll spend a week or two talking about confocal endoscopes. After that, we'll spend a week or two talking about new tricks (including tricks that my students and I are working on) for making microscopes with resolution that scientists used to think was impossible. We'll also have presentations by a few other professors, and finish the quarter with a few weeks of student presentations.