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 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
Download:

LineScan

Automated line scan for quantification of correlations between intracellular fluorescence intensity and cell edge velocity

In collaboration with Tsygankov Lab and Elston Lab
Published in Methods. 2014 Mar 15;66(2):162-7. doi: 10.1016/j.ymeth.2013.08.025. | [ncbi pmc]
Download LineScan zip file 831 KB

EdgeProps

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.

In collaboration with Tsygankov Lab

Publications:

Download: EdgeProps zip file 3.0 MB

Protein engineering

SPELL

In collaboration with Dokholyan Lab
SPELL server: https://dokhlab.med.psu.edu/spell/login.php

Loopology

Published in Nat Protoc. 2019;Jun;14(6):1863-1883. doi: 10.1038/s41596-019-0165-3.

Analyzing cellular morphodynamics

SquigglyMorph

Automated classification of cellular morphodynamics

In collaboration with Tsygankov Lab and Elston Lab
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

Publications:

Versions:

SegmentMe

Automated segmentation and tracking of tightly packed cells with simple geometry; allows quantification of intracellular clustering

In collaboration with Tsygankov Lab and Elston Lab
Published in Methods Cell Biol. 2014;123:409-27. doi: 10.1016/B978-0-12- 420138-5.00022-7. | [ncbi PMC]
download SegmentMe zip file 26.06 MB

Versions:

CellGeo

Multi-module platform for cell protrusion analysis: automated identification and tracking of protrusions of different scales and with arbitrarily complex geometry

In collaboration with Tsygankov Lab and Elston Lab
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]

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

Software for segmentation and analysis of cellular adhesions.

In collaboration with Gomez Lab
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

Microscope automation and high content screening

High Content Screening

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.

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

Digital Autofocus

Digital autofocus methods for automated microscopy.

Published in Methods Enzymol., 414:620-632, 2006.
Download:

Section Title for Denis' paper

Denis' Frontier Paper - Correcting Artifacts in Ratiometric Biosensor Imaging

Noise Correction Factor Processing

Published in Front. Cell Dev. Biol. 2021:9(2311):fcdb.685825. doi: 10.3389/fcell.2021.685825 | [NCBI pmc]

MATLAB scripts for NCF application are available at https://github.com/tsygankov-lab/NoiseCorrectionFactor.

Section Title for Binder-Tag paper

Binder-Tag - Biosensors Based on Peptide Exposure Show Single Molecule Conformations in Live Cells

Some particular name for the code?

Published in Cell 2021:Oct 11. doi: ??

Main components of this code are available at https://github.com/mikepab/binder-tag.

Collaborator Labs with useful softare

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.

Dokhoyan Lab (https://dokhlab.med.psu.edu/#/tools/)

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:

Kuhlman Lab (http://klab.web.unc.edu/software/)

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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~ Updated 10/01/2021

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