THE software collaboration (Tsygankov Hahn Elston)
Software resulting from a collaboration of the Tsygankov, Hahn, and Elston Labs.

1. CellGeo (multi-module platform for cell protrusion analysis: automated identification and tracking of protrusions of different scales and with arbitrarily complex geometry).

Includes the following modules:

• MovThresh (simple and convenient way to threshold and visualize cell edge, allows automated, assisted, and manual masking with variable threshold at each time frame.) [download MoveThresh zip file 2.0 MB]
• BisectoGraph (maps arbitrarily polygon on a tree graph required for FiloTrack and ConeTrack modules, allows interactive study of protrusion geometry and the underlying cell body.) [download BisectoGraph zip file 95KB]
• FiloTrack (identifies and tracks filopodia-like protrusions based on user- specified constrains.) [download FiloTrack zip file 2.15 MB]
• ConeTrack (identifies and tracks neural-grows-cone-like protrusions based on user-specified constrains.) [download ConeTrack zip file 51.89 MB]
• ProActive (quantifies protrusion/retraction activity of lamellipodia-like protrusions; does NOT require BisectoGraph mapping.) [download ProActive zip file 2.33 MB]

Published here: J Cell Biol. 2014 Feb 3; 204(3): 443-60. doi: 10.1083/jcb.201306067. [ncbi pmc]

Used in the following publications:

• Dev Cell. 2014 Feb 24;28(4):394-408. doi: 10.1016/j.devcel.2014.01.015. [ncbi pmc]
• Nat Chem Biol. 2014 Apr;10(4):286-90. doi: 10.1038/nchembio.1477. [ncbi pmc]

Versions:

• V.1 works for earlier MATLAB versions before 2014 major changes in its handling of graphics. [download CellGEO zip file 58.38 MB]
• V.2 works for later MATLAB versions after 2014 major changes in its handling of graphics. [download CellGEO 2014 zip file 58.38 MB]

Additions (as requested by extramural users): Code for post-processing and customized visualization of FiloTrack results. [download additional FiloTrack zip file 5.26 MB]

2. LineScan (automated full-edge line-scan for quantification of correlations between intracellular fluorescence intensity and cell edge velocity). [Zip file download link 831 KB]

Published here: Methods. 2014 Mar 15;66(2):162-7. doi:10.1016/j.ymeth.2013.08.025.

3. SquigglyMorph (automated classification of cellular morphodynamics) [download SquigglyMorph zip file 256 KB]

Published here: Methods Cell Biol. 2014;123:409-27. doi: 10.1016/B978-0-12- 420138-5.00022-7.

Used in the following publications:

• Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12420-5. doi: 10.1073/pnas.1404487111. [ncbi pmc]

Versions:

• V.1 works for earlier MATLAB versions before 2014 major changes in its handling of graphics. [download SquigglyMorph zip file 225 KB]
• V.2 works for later MATLAB versions after 2014 major changes in its handling of graphics. [download SquigglyMorph 2014 zip file 225 KB]

4. SegmentMe (automated segmentation and tracking of tightly packed cells with simple geometry; allows quantification of intracellular clustering.) [download SegmentMe zip file 26.06 MB]

Published here: Methods Cell Biol. 2014;123:409-27. doi: 10.1016/B978-0-12- 420138-5.00022-7.

Versions:

• 2D: main version [download 2D SegmentMe zip file 26.0 MB]
• 3D: extension of the 2D processing [download 3D SegmentMe zip file 26.0 MB]

5. EdgeProps (A method for correlative analysis of signal activity, edge velocity, protrusion persistence and orientation; the approach is not sensitive to roughness of the cell edge, i.e. overcomes the limitations of LineScan and Gaudenz Box methods; includes full-edge kymograph and other representations of the edge dynamic.) [download EdgeProps zip file 3.0 MB]

Published here: J Am Chem Soc. 2016 Mar 2;138(8):2571-5. doi: 10.1021/jacs.5b09764

 

Biosensor image analysis

We are building a comprehensive software package for biosensor analysis by combining material from sections 1-4 above with older routines described in the following older methods articles:

For genetically encoded FRET biosensor imaging, please see the following methods articles:

• Biosensors for Characterizing the Dynamics of Rho Family GTPases in Living Cells. Curr. Prot. Cell Biol., 46: Chp.14.11, 2010.
• Design and Optimization of Genetically ncoded Fluorescent Biosensors: GTPase Biosensors. Methods Cell Biol., 85:63-81, 2008.

An older methods article with information re photobleach correction and use of dye-based biosensors:

• Imaging and Photobleach Correction of Mero-CBD, Sensor of Endogenous Cdc42 Activation. Methods Enzymol., 406:140-156, 2006.

 

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~ Updated 02/17/2021