Export for DiffusionLab

DiffusionLab supports the import of tracks from DoM v.1.1.6 and Localizer for Igor Pro. Support requests for formats can be sent to the developers.

DoM v.1.1.6

DoM is an ImageJ plugin for localization and tracking of single-molecule fluorescence time lapse movies. The software is freely available here. The results can be exported via the ImageJ “Results” table. The steps are the following:

  1. Open your movie in ImageJ

  2. Analyze > DoM v.1.1.6 > Detect molecules and perform “Detect molecules and fit” with the optimized settings for your system. Use a “fitting iterations number” of 5

  3. Analyze > DoM v.1.1.6 > Link Particles to Tracks

  4. Go to the “Results” table and go to File > Save As and save the table as .csv file

Macros are available in the group for batch localization and linking into tracks.

Localizer for Igor Pro

Localizer is a plugin for Igor Pro for localization and tracking of single-molecule fluorescence time lapse movies. The software is freely available here. Tracks can be computed and exported following:

  1. Localizer > Read CCD data > Read CCD data from disk…

  2. Press >> on the movie viewer and perform Localization and Tracking

  3. Localizer > Manipulate Particle Tracks > Save tracks to text file…

Supported Localization algorithms are:

  • Gaussian fitting

  • Gaussian fitting (fixed width)

  • Ellipsoidal Gaussian fitting

  • MLEwG

Warning

The localization algorithm is recognized by the number of columns in the output file. If this changes, the columns are interpreted incorrectly.

COMSOL

COMSOL is a commercial software packing for multiphysics modelling and allows single-particle trajectory simulation. For this, the Particle tracing module should be installed. Tracks can be exported follwing:

  1. To do!

Warning

COMSOL exports the coordinates in three dimensions. The functionality of DiffusionLab for 3D trajectories is limited and some track properties are only computed in the XY-plane. A warning in the MATLAB log window appears when this occurs, and explains which track properties have been affected.