software

Biosensor Processing Software 2.1

This matlab software package allows processing of raw ratiometric biosensor images 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 (3.8 Mb)

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

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 1.1.1, 25.5 Mb)

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).

u-track

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.

Download (3.4 MB) - now with improved speed and motion modeling.

For more information, please see Jaqaman et al., Nature Methods 5, pp. 695-702 (2008).

Spot detection

Matlab software for the detection of diffraction-limited or other spot-shaped fluorescent signals in a noisy background. The algorithm is based on [Olivo-Marin, J.-C., Pattern Recognition 35, pp. 1989-1996 (2002)]. An example is included in the download.

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