User:TheLarry/Notebook/Larrys Notebook/2009/11/16/Quantitative Comparison of Algorithms for Tracking Single Fluorescent Particles

An interesting paper written in 2001 by Cheezum, Walker, and Guilford from University of Virginia. They look at the pros and cons for three different types of single molecule tracking. But that isn't why i read this paper.

The important part is they talk about making a simulated movie to track something in. Exactly how i am doing it, and for the most part i am following in their footsteps. Except in a couple of points:

1. They convolute the molecule they are tracking with the point spread function, the airy disk. For a point this is a scaled version or so they say. I am not sure what that means exactly yet.
   • But i could just convolute the rectangular microtubule with the point spread function and save me the trouble of the fluorescence dots. Just a thought. Koch thought of this earlier but i dismissed it. Figuring the dot was more realistic. I am still there but this is another option.
2. They turn this convolution into a higher resolution image. Higher than their CCD camera can take
   • They then integrate over a bunch of these higher resolution images to make a lesser resolved image. I do make a higher resolution image (in nm) then switch it over to pixels, but i don't integrate a bunch of these higher resolved points. It is probably better if i did. I have to look into this tomorrow.
3. They also put in shot noise. This is the first i hear of this term, but i think it means the noise created by a CCD camera. Apparently the noise increases as the number of photons it collects increases. They simulated this by picking a value for the intensity of the pixel based on a Poisson distribution of mean N where N is the level from the previous bullet.
   • I started to implement this today, but i am much more crude and my mean for the poisson distribution probably needs to be scaled better.

I haven't read this paper well, outside of the early stuff written above since that interests me the best. but there seems to be some other papers to look at tomorrow when i have access to more papers.

1. Saxton Jacobson 1997
   • An "excellent" review on single particle tracking
2. Young 1996
   • Something to do on the Airy function or point spread function
3. Shot Noise
   • Ryan 1990
   • Papoulis 1984
   • Press 1997