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:
- J Am Chem Soc. 2016 Mar 2;138(8):2571-5. doi: 10.1021/jacs.5b09764. | [ncbi pmc]
- Methods Mol Biol. 2018;1821:47-56. doi: 10.1007/978-1-4939-8612-5_4 | [ncbi pmc]
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:
- Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12420-5. doi: 10.1073/pnas.1404487111. | [ncbi pmc]
- Methods Cell Biol. 2014;123:409-27. doi: 10.1016/B978-0-12- 420138-5.00022-7 | [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]
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:
- 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]
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:
- 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 a 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 neuronal growth cone protrusions based on user-specified constraints.) [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]
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]
- J Cell Biol. 2014 Feb 3; 204(3): 443-60. doi: 10.1083/jcb.201306067. | [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]
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:
- Fluctuation analysis of activity biosensor images for the study of information flow in signaling pathways. Methods Enzym., 519:253-76, 2013.
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:
- Biosensor FRET detection by the phasor approach to Fluorescence Lifetime Imaging Microscopy (FLIM). Microsc Res Tech 75(3): 271-81, 2012.
- Millisecond spatiotemporal dynamics of FRET biosensors by the pair correlation function and the phasor approach to FLIM. Proc Natl Acad Sci U.S.A. 110: 135-40, 2013.
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.
back to molecular imaging tools / software page
~ Updated 10/01/2021