Correct particle intensities in Trackmate

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Hello. We are using the Trackmate plugin to track single fluorescent protein molecules in living cells. Apart from the location of the spots, we are also interested in their intensity, because that reports on the proteins being monomeric, dimeric etc. What I noticed is that the intensity values that I can access, such as mean, median, max or total intensity, all represent pixel-values, and they all suffer from “pollution” by autofluorescence of the cells that decays (bleaches) gradually over time. Considering that the software fits a Gaussian funcion to the spot, I was wondering if it would be possible to log the height or the volume of the Gauss, because that would be background-corrected, I presume. Other suggestions are welcome.


Hi @yves_bollen

Actually TrackMate does not fit a gaussian on spots.

We detect spot by LoG (or DoG), with a sub-pixel localization scheme, and we measure the intensities within the radius specified by the user.