TrackMate calculated SNR lower than expected


I have been using the spot statistics in TrackMate to find the SNR of my tracked spots. I’ve noticed that spots are tracked well for SNR values way below the ‘critical’ value (4) that is stated in the papers. I have tried manually calculating it using the equations and it comes out different to what TrackMate calculates.

I’ve attached a bead that is tracked relatively well where the SNR according to TrackMate is 0.8-1.2 but manual calculations give me a much higher numbers.


There’s different definitions of signal-to-noise ratio (SNR). How did you calculate the SNR manually?

Looking at the source of SpotContrastAndSNRAnalyzer, the SNR is determined by taking the difference of means of two rings around the spot center (0 <= r <= r_{spot} and r_{spot} <= r <= 2*r_{spot}) and dividing this by the standard deviation within the spot radius:

@tinevez might be able to comment further.