hahn lab

software

 

Analyzing biosensor data

Hahn Lab Biosensor Imaging Package

A complete package with GUI for imaging of biosensors. Incorporates the photobleach correction program from below and much more. We will be providing updated versions on github and here.
Download: 2dfretimgproc-master-v1.zip [5.7 MB] .

Photobleach Correction

Published in Methods Enzymol., 406:140-156, 2006 [PDF]
Download:

LineScan

In collaboration with Denis Tsygankov, Tim Elston
Published in Methods. 2014 Mar 15;66(2):162-7. doi:10.1016/j.ymeth.2013.08.025.
download LineScan zip file 831 KB
Automated line scan for quantification of correlations between intracellular fluorescence intensity and cell edge velocity

EdgeProps

In collaboration with Denis Tsygankov
Published in J Am Chem Soc. 2016 Mar 2;138(8):2571-5. doi: 10.1021/jacs.5b09764
download EdgeProps zip file 3.0 MB

A method for correlative analysis of signaling activity, edge velocity, protrusion persistence and orientation; the approach is not sensitive to roughness of the cell edge. It includes kymographs and other representations of edge dynamics.

Protein Engineering

SPELL - coming soon

Loopology - coming soon

Analyzing cellular morphodynamics

SquigglyMorph

In collaboration with Denis Tsygankov, Tim Elston
Published in Methods Cell Biol. 2014;123:409-27. doi: 10.1016/B978-0-12- 420138-5.00022-7 [ncbi pmc]
download SquigglyMorph zip file 256 KB
Automated classification of cellular morphodynamics

Publications:

Versions:

SegmentMe

In collaboration with Denis Tsygankov, Tim Elston
Published in Methods Cell Biol. 2014;123:409-27. doi: 10.1016/B978-0-12- 420138-5.00022-7.
download SegmentMe zip file 26.06 MB
Automated segmentation and tracking of tightly packed cells with simple geometry; allows quantification of intracellular clustering

Versions:

CellGeo

in collaboration with Denis Tsygankov, Tim Elston
For further development of CellGeo see the Tsygankov lab website
Published in J Cell Biol. 2014 Feb 3; 204(3): 443-60. doi: 10.1083/jcb.201306067. [ncbi pmc]
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:

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]

Focal Adhesion Analysis Server

In collaboration with Shawn Gomez
Published in PLoS One. 2011;6(7):e22025. | doi: 10.1371/journal.pone.0022025 | [NCBI PMC]
Web server: http://faas.bme.unc.edu
Download Code: https://github.com/gomezlab/focal_adhesions
Software for segmentation and analysis of cellular adhesions.

Microscope automation and high content screening

High Content Screening

Publshed in Curr. Prot. Cell Biol., 65: Chp. 14.15.1–14.15.31, 2014.
Download:

A very useful high content screening assay for biosensor validation, or for using a well-characterized biosensor as a readout for effects of upstream molecules, used to optimize biosensors, or to use biosensor readouts as endpoints in high content screening assays.

Digital Autofocus

Published in Methods Enzymol., 414:620-632, 2006.
Digital autofocus methods for automated microscopy.
Download:

Other Labs

CISMM: Computer Integrated Systems for Microscopy and Manipulation (http://cismm.web.unc.edu/)

An NIH center integrating methods to visualize and manipulate force in cell biology.

Danuser Lab (http://www.utsouthwestern.edu/labs/danuser/)

See the Danuser Lab software page for automated biosensor image processing software and other software for analysis of signaling pathways based on biosensors and optogeneics.
Ref:

Elston Lab (http://elstonlab.web.unc.edu)

Gomez Lab (http://gomezlab.bme.unc.edu)

Gratton Lab (http://www.lfd.uci.edu)

See the Gratton lab software page for SimFCS, a comprehensive image processing solution
Refs:

Tsygankov Lab (https://pwp.gatech.edu/denislab/)

See the Tsygankov lab website for image analysis software and further development of CellGeo.

The Integrative Systems Biology Lab, directed by Dr. Denis Tsygankov, focuses on integrating experimental and computational methods (involving modeling, simulations, and novel computer vision techniques) to gain a systems-level understanding of complex biological processes. The emphasis is made on biomechanical aspects of physiological phenomena across scales from molecules to cells to tissues.


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