TRABI is an analysis tool for ImageJ that allows the determination of accurate single-molecule fluorescence intensities independent of the axial position. It analyses single-molecule TIF-stacks (e.g. dSTORM, PALM acquisitions) on the basis of localization files from rapidSTORM, ThunderSTORM, or PeakFit. Besides intensity estimation, which is important for the characterization of novel dyes and switching buffers, it also allows to extract 3D information from 2D images. The software code is open-source and can be downloaded (by clicking on the version number).

VersionChangesRelease Date
1.2Batch mode bug fix19 Apr 2017
1.1Batch processing option, CSV file handling, editable exclusion zone, faster analysis, pixel interpolation in rapidSTORM11 Apr 2017
1.021 Nov 2016

The corresponding paper can be found here. For bug reports, suggestions and improvements please contact Sebastian.


  • TRABI v1.0 only handles TXT files, not CSV files (optional ThunderSTORM output). Simply rename your file test.csv to test.txt to avoid the error: beginIndex>endIndex in line 508


ImageJ/Fiji macro for visualizing single-molecule localization files. Renders images and shows localizations in raw TIF stacks. Supports rapidSTORM and ThunderSTORM localization files by default and any other after manual specification (user-defined).

VersionChangesRelease date
1.1Minor improvements12 Jul 2019
1.013 Mar 2019

The corresponding paper can be found here.


HyphaTracker is an ImageJ toolbox for the temporal analysis of spore germination in filamentous fungi. Input data is a TIF stack acquired with optical microscopes.

VersionChangesRelease date
1.012 Jan 2018

The corresponding paper can be found here.