Gaussian Localization for TrackMate

This software plugin refines molecular localization in microscopy images by performing Gaussian fitting on object positions initially estimated using the center of mass. While center-of-mass detection provides a fast and approximate estimate of molecular positions, it is often limited by noise and pixelation effects. The Gaussian fitting step models the intensity profile of each molecule as a 2D Gaussian, enabling sub-pixel accuracy and improved localization precision. This approach enhances the reliability of position estimates, making it particularly useful for quantitative fluorescence microscopy and single-molecule tracking applications.

Example of localization improvement: (red) localization using the TrackMate default strategy, (yellow) the localization after performing the Gaussian fitting.

Download .jar

How to run

• Run plugin “GaussFit to TrackMate Tracks” which can be found in Plugins’ menu of Fiji in the section “BioAI”

• Specify the desired parameters shown in the dialog below:

• As the next step, select the folder with the .XML files/tracks. One should select a folder that contains images and another sub-folder named “TRACKS” with the .xml files inside. The results of processing will be also stored in the TRACKS folder with extension “.Gauss.xml”