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Table 1 Summary of the main properties of the open source softwares for 4D tracking

From: Visual4DTracker: a tool to interact with 3D + t image stacks

Software ilastik [9] DiaTrack [8] TrackMate [10] Visual4DTracker (proposed)
Manual tracking YES: after segmentation, clicking frame by frame the moving object NO NO YES
Automatic tracking YES: it uses the Least Square, Distance association method YES: after segmentation, it uses the Least Square Distance association method YES: after segmentation, it uses the Least Square Distance association method NO
Single particle tracking YES NO NO YES
Multiple particle simultaneous tracking YES YES YES NO
Particle occlusion handling YES: it is possible to manually define split events of single objects NO YES: it automatically searches for multiple objects split events NO
Pre-processing YES (several filters) YES (only Gaussian Filter, luminosity threshold) NO YES (several filters, user defined functions)
Proof-reading NO NO YES: it is only possible to load the traces and to modify the tracking parameters YES
Tracking processing NO YES: it is possible to compute kinematic parameters from the traces NO NO
3D tracking visualization NO: only 2D multiple orthogonal layers representation NO: only 2D multiple orthogonal layers representation NO: 2D multiple layers representation surfable in quote and frames YES
3D data reconstruction YES YES YES YES
Manual tracking in 3D visualization NO NO NO YES
User developped pre/post processing functions NO NO NO: not directly, however the software is a Fiji plug-in YES: it is possible to upload custom functions in MATLAB
Output File in .hdf5 format (or others) File in .txt format trajectories and data and .eps format for the images File in .xml format File in .xml format
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