Software

Software

Particle tracking
Quantitative ratiometric image analysis
Traction force microscopy
Clathrin-mediated endocytosis analysis
Quantitative fluorescent speckle microscopy
DeBias
Decoupling global biases and local interactions between cell biological variables

u-track 2.0                                         

u-track is a multiple-particle tracking MATLAB software that is designed to (1) track dense particle fields, (2) close gaps in particle trajectories resulting from detection failure, and (3) capture particle merging and splitting events resulting from occlusion or genuine aggregation and dissociation events. Its core is based on formulating correspondence problems as linear assignment problems and searching for a globally optimal solution.

  • Version 2.2 adds parallel processing functionality for multi-movie datasets when using the GUI.
  • Version 2.1 enables the analysis of movies stored on an OMERO server
  • Version 2.0 includes two new tracking applications: microtubule plus-end tracking (previously distributed as plusTipTracker) and nuclei tracking
  • A third optional processing step has been added to the analysis workflow, track analysis, with two methods: motion analysis and microtubule plus-end classification

Download (Version 2.2.1, 35.5 MB) - now with improved speed and motion modeling.    
For more information, please see Jaqaman et al., Nature Methods 5, pp. 695-702 (2008). Besides basic particle tracking, the software supports the features described in Applegate et al. J. Struct. Biol. 176(2):168-84. 2011 for tracking microtubule plus end markers; and in Ng et al. J. Cell Biol. 199(3):545-63. 2012 for tracking fluorescently-labeled cell nuclei.


Biosensor Processing 2.1               

This MATLAB software package allows processing of raw ratiometric biosensor images (for example based on FRET) into fully corrected "ratio maps" or "activation maps" — images showing the localized activation of the biosensor. This includes application of all necessary image corrections needed for quantitative widefield imaging of ratiometric biosensors.
New in Version 2.1:

  • Added support for movie relocation
  • Implemented a graphical interface for preparing data
  • Added a preview option when manually thresholding channels
  • Added graphical interfaces for the transformation creation and bleedthrough coefficients calculation
  • Included the ratio movie creation within the output process
  • Fixed various bugs (correction image display...)

Download (Version 2.1.1, 39.1 MB)

For more information, please see Hodgson et al., Curr Protoc Cell Biol. 14.11 (2010).


TFM                              

TFM (Traction Force Microscopy) is a MATLAB software that reconstructs traction forces of cells adhered on elastic gel doped with beads. The software quantifies the deformation of the gel by image-based tracking of the beads from pairs of images, one displaying in the deformed and displaying the relaxed substrate. Traction force reconstruction is accomplished via L1-regularization, which is particularly good for identifying traction from small adhesions. It generates traction magnitude heat-maps as well as traction vector fields as outputs. The software additionally supports conventional L2-based BEM (Boundary Element Method) and FTTC (Fourier Transform Traction Cytometry).

Download (Version 1.1.3, 37 MB)

The innovative parts of the reconstruction algorithms are published in Han et al., Nature Methods (2015)


cmeAnalysis                         

cmeAnalysis (clathrin-mediated endocytosis analysis) is a MATLAB software package for the quantification of clathrin-coated pit dynamics from fluorescence time-lapse data. The functionalities provided include highly sensitive detection, tracking (based on u-track), master/slave detection for multi-channel data, intensity-based classification of coated structures, and lifetime analysis. Additionally, the package includes a graphical user interface for inspection of analysis results from individual movies.
The download includes a user guide, and a test data set is available separately.

Release notes: includes improvements to graphical and console output.

For more information, please see Aguet et al., Dev. Cell 26(3), pp. 279-291, 2013.


 QFSM                                             

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). 


 DeBias                                          

Global bias is often a neglected in interpretation of co-localization, but encapsulates fundamental mechanistic insight into cellular behavior. DeBias decouples the global bias from direct interactions, allowing global bias to be considered as a second measurement for the analysis of complex relations between cellular variables.

Source code available here: https://github.com/DanuserLab/DeBias

DeBias data analysis webserver: https://debias.biohpc.swmed.edu/ 

For more information, please see Zaritsky et al., eLife, 10.7554/eLife.22323 (2017)



 *Unsupported Packages



 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*

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*                            

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).