hahn lab

Analyzing cellular morphodynamics and biosensor activity

 

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:

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

Used in the following publications:

Versions:

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). [download LineScan zip file 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:

Versions:

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:

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:

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

 

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