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QuimP Software

QuimP software, a set of plugins for ImageJ, has been developed by Till Bretschneider and Richard Tyson to quantify spatio-temporal patterns of fluorescently labeled proteins in the cortex of moving cells.

QuimP was first described in Dormann et al., 2002. For information on the classic version, now called QuimP1, please follow this link.

QuimP2 which was developed in collaboration with Leonard Bosgraaf (Bosgraaf et al., 2009) introduced a new method to correlate local cortical fluorescence with membrane movement. An obsolete QuimP2 installation package can be downloaded here (Unzip the archive and move the contents of the two folders according to their directory name. The help icon that appears when launching the QuimP toolbar provides an in depth explanation of how to use the associated plugins and the individual parameters). An addon for pseudopod analysis resulted in QuimP3 which however is not officially supported by the main QuimP development team (contact Leonard Bosgraaf for help instead).

QuimP11b is now available that adds compatibility for ImageJ (tested with 1.49a) and MATLAB 2014. It also provides batch processing features, improvements to the segmentation GUI, and added stability for contour mapping (see the included help file for details). Click here to download QuimP11b.

QuimP11 supplants QuimP10. It has a completely new semi-automated segmentation interface, a greatly improved boundary tracking method based on Richard Tyson's ECMM method, muti-channel support, and extended documentation. This version remains backward compatible with QuimP10 output.
QuimP is free software, but we ask you to register by filling out the form on the download page. Monitoring the demand is essential to apply for continued funding of QuimP. We most welcome any feedback which will help us to make QuimP better. Also, please let us know what you use it for.

 

 

QuimP has been used in the following labs:

Heidi Welch, the Babraham Institute

Anna-Karin E. Johnsson, Yanfeng Dai, Max Nobis, Martin J. Baker, Ewan J. McGhee, Simon Walker, Juliane P. Schwarz, Shereen Kadir, Jennifer P. Morton, Kevin B. Myant, David J. Huels, Anne Segonds-Pichon, Owen J. Sansom, Kurt I. Anderson, Paul Timpsone, Heidi C.E. Welch
The Rac-FRET Mouse Reveals Tight Spatiotemporal Control of Rac Activity in Primary Cells and Tissues
Cell Reports. 2014 March 27;6(6):1153-64

Graham Ladds, Warwick Medical School

Bond M, Croft W, Tyson R, Bretschneider T, Davey J, Ladds G.
Quantitative analysis of human ras localization and function in the fission yeast Schizosaccharomyces pombe.
Yeast. 2013 Apr;30(4):145-56

Christoph Ballestrem, University of Manchester

Carisey A, Tsang R, Greiner AM, Nijenhuis N, Heath N, Nazgiewicz A, Kemkemer R, Derby B, Spatz J, Ballestrem C.
Vinculin regulates the recruitment and release of core focal adhesion proteins in a force-dependent manner.
Curr Biol. 2013 Feb 18;23(4):271-81.

Daniel Wuestner, University of Southern Denmark

Wüstner D, Faergeman NJ.
Spatiotemporal analysis of endocytosis and membrane distribution of fluorescent sterols in living cells.Histochem Cell Biol. 2008 Nov;130(5):891-908.

Wüstner D.
Plasma membrane sterol distribution resembles the surface topography of living cells.
Mol Biol Cell. 2007 Jan;18(1):211-28.

Len Stephens, Babraham Institute, Cambridge

Ferguson, G.J., Milne, L., Kulkarni, S., Sasaki, T., Walker, S., Andrews, S., Crabbe, T., Finan, P., Jones, G., Jackson, S., Camps, M., Rommel, C., Wymann, M., Hirsch, E., Hawkins, P. & Stephens, L.
PI(3)Kgamma has an important context-dependent role in neutrophil chemokinesis.
Nat Cell Biol, 2007, Vol. 9(1), pp. 86-91

Rob Kay, MRC LMB, Cambridge

Zanchi, R., Howard, G., Bretscher, M.S. & Kay, R.R.
The exocytic gene secA is required for Dictyostelium cell motility and osmoregulation.
J Cell Sci, 2010, Vol. 123(Pt 19), pp. 3226-3234

Guenther Gerisch, Max-Planck-Institute of Biochemistry

Dalous, J., Burghardt, E., Mueller-Taubenberger, A., Bruckert, F., Gerisch, G. & Bretschneider, T.
Reversal of cell polarity and actin-myosin cytoskeleton reorganization under mechanical and chemical stimulation.
Biophys J, 2008, Vol. 94(3), pp. 1063-1074

Etzrodt, M., Ishikawa, H.C.F., Dalous, J., Mueller-Taubenberger, A., Bretschneider, T. & Gerisch, G.
Time-resolved responses to chemoattractant, characteristic of the front and tail of Dictyostelium cells.
FEBS Lett, 2006, Vol. 580(28-29), pp. 6707-6713

Bretschneider, T., Jonkman, J., Köhler, J., Medalia, O., Barisic, K., Weber, I., Stelzer, E.H.K., Baumeister, W. & Gerisch, G.
Dynamic organization of the actin system in the motile cells of Dictyostelium.
J Muscle Res Cell Motil, 2002, Vol. 23(7-8), pp. 639-649

Mueller-Taubenberger, A., Bretschneider, T., Faix, J., Konzok, A., Simmeth, E. & Weber, I.
Differential localization of the Dictyostelium kinase DPAKa during cytokinesis and cell migration.
J Muscle Res Cell Motil, 2002, Vol. 23(7-8), pp. 751-763

Kees Weijer, University of Dundee

Sobczyk GJ1, Wang J2, Weijer CJ1. SILAC-based proteomic quantification of chemoattractant-induced cytoskeleton dynamics on a second to minute timescale.
Nat Commun. 2014 Feb 26;5:3319. doi: 10.1038/ncomms4319.

Dormann, D., Weijer, G., Dowler, S. & Weijer, C.J.
In vivo analysis of 3-phosphoinositide dynamics during Dictyostelium phagocytosis and chemotaxis.
J Cell Sci, 2004, Vol. 117(Pt 26), pp. 6497-6509

Peter van Haastert, University of Groningen

Haastert, P.J.M.V.
A model for a correlated random walk based on the ordered extension of pseudopodia.
PLoS Comput Biol, 2010, Vol. 6(8)

Haastert, P.J.M.V. & Bosgraaf, L.
The local cell curvature guides pseudopodia towards chemoattractants.
HFSP J, 2009, Vol. 3(4), pp. 282-286

Haastert, P.J.M.V. & Bosgraaf, L.
Food searching strategy of amoeboid cells by starvation induced run length extension.
PLoS One, 2009, Vol. 4(8), pp. e6814

Bosgraaf, L. & Haastert, P.J.M.V.
Navigation of chemotactic cells by parallel signaling to pseudopod persistence and orientation.
PLoS One, 2009, Vol. 4(8), pp. e6842

Bosgraaf, L. & Haastert, P.J.M.V.
The ordered extension of pseudopodia by amoeboid cells in the absence of external cues.
PLoS One, 2009, Vol. 4(4), pp. e5253

Bosgraaf, L., Keizer-Gunnink, I. & Haastert, P.J.M.V.
PI3-kinase signaling contributes to orientation in shallow gradients and enhances speed in steep chemoattractant gradients.
J Cell Sci, The Netherlands., 2008, Vol. 121(Pt 21), pp. 3589-3597

Bosgraaf, L., Waijer, A., Engel, R., Visser, A.J.W.G., Wessels, D., Soll, D. & van Haastert, P.J.M.
RasGEF-containing proteins GbpC and GbpD have differential effects on cell polarity and chemotaxis in Dictyostelium.
J Cell Sci, 2005, Vol. 118(Pt 9), pp. 1899-1910

 

 

Papers describing the development of QuimP

Bosgraaf, L. & Haastert, P.J.M.V.
Quimp3, an automated pseudopod-tracking algorithm.
Cell Adh Migr, 2010, Vol. 4(1), pp. 46-55

Tyson, R.A., Epstein, D.B.A., Anderson, K.I. & Bretschneider, T.
High resolution tracking of cell membrane dynamics in moving cells: An electrifying approach.
Math. Model. Nat. Phenom., 2010, Vol. 5(1), pp. 34-55

Bosgraaf, L., van Haastert, P.J.M. & Bretschneider, T.
Analysis of cell movement by simultaneous quantification of local membrane displacement and fluorescent intensities using Quimp2.
Cell Motil Cytoskeleton, 2009, Vol. 66(3), pp. 156-165

Dormann, D., Libotte, T., Weijer, C.J. & Bretschneider, T.
Simultaneous quantification of cell motility and protein-membrane-association using active contours.
Cell Motil Cytoskeleton, 2002, Vol. 52(4), pp. 221-230


QuimP GUI

cell1_track.png

Contour Mapping