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3D Morphological Motif Detection


Particle Tracking in 3D


Particle tracking


Quantitative ratiometric image analysis


Traction force microscopy


Clathrin-mediated endocytosis analysis


Decoupling global biases and local interactions between cell biological variables


 *Unsupported Packages


Quantitative Fluorescent Speckle Microscopy*

QFSM (Quantitative Fluorescent Speckle Microscopy) is a MATLAB software for quantifying the rate of polymer assembly, disassembly and flow across the entire leading edge in constitutively motile cells from fluorescent speckle microscopy movies. It identifies and computationally tracks speckles and utilizes their location, appearance, and disappearance to derive network flows and assembly/disassembly maps.

Download (Version 1.0.1, 32.7 MB)

For more information, please see Mendoza et al., Current Protocols in Cytometry 62:2.18.1–2.18.26 (2012).


 3D cell shape and migration*

This software allows the analysis of cell shape (both branching and local surface curvature) and motion, and correlation between these shape and motion parameters and subcellular fluorescence localization. It does not have a point-and-click graphical user interface and requires some familiarity with MATLAB, as well as specific data formats. Some features require third-party software (Imaris).

Download software (Version 1.0, 2.6 MB)

Download example data (300 MB)

For more detail, see the Users Guide or Elliott et al., Nat Cell Bio 17, 137-147 (2015)


plusTipTracker is a MATLAB software package for tracking the full dynamics of microtubules based on +TIP marker live cell image sequences. Concepts are related to the ClusterTrack software; however, the tracking builds on the algorithms implemented in the u-track software. The package can be operated via a convenient graphical user interface. It contains a sizable set of service functions for data visualization and statistical processing of parameters of microtubule dynamics. We strongly recommend the download of this package for the purpose of microtubule tracking. The download bundle includes a user's guide in the form of a Technical Report and complete documentation of all the functions in the package.

Download (Version 1.1.4, 25.4 MB)

Note: a new version of plusTipTracker will be released in 2013 with a new interface. The current interface will not be supported anymore.
Note: The functionality of plusTipTracker is now integrated with the new release of u-track (Version 2.0). While you are welcome to still download this version of plusTipTracker, we do no longer support the interface.



ClusterTrack is the MATLAB software developed for the purpose of proving the principle that full microtubule dynamics can be tracked and inferred based on +TIP marker live cell image sequences only. The download bundle contains the MATLAB programs documented by a software guide. It also contains multi-color movies of EGFP-EB1 and mCherry-tubulin used for validation. Note, this package will not be maintained and it is not set up as a user–friendly software. We strongly recommend the download of the plusTipTracker package for practical microtubule analyses.

Download (147.4 MB)

For more information, please see Matov et al., Nature Methods 7, pp. 761-768 (2010).