No, that’s not what I’m looking for.

Let me try to clarify:

I’m looking for the localization noise for each point. This would probably be linked to the particle detection in each frame. Essentially this is the uncertainty in the determination of the coordinates of each point.

I’m using this value in calculating diffusion coefficients from mean-square displacement values using the following equation:

MSD(τ) = 4Dτ + 4σ^2, where MSD is mean-square displacement, τ is the time-lag, D is the diffusion coefficient, and σ is the localization noise that I’m looking for.

This is important for my purposes because the diffusion of the particles that I’m looking at can be on the same length scale as the typical localization error for most SPT algorithms, so to accurately calculate D, it’s necessary to know σ.

(This concept might be better explained in this paper: https://journals.aps.org/pre/abstract/10.1103/PhysRevE.82.041914)

I was previously able to get this value out for all of the detected points when using the MATLAB implementation of u-Track, but I wanted to switch to TrackMate, and I was hoping to get out the same parameters here.

I hope that this somewhat clarifies what I’m looking for, and thanks for taking the time to respond so far!