About

QuimP software, a set of plugins for ImageJ, has been developed by Till Bretschneider, Richard Tyson and Piotr Baniukiewicz (current developer) 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).

QuimP3 is currently under development. It supports user plugins, other segmentation algorithms, image pre-processing and offers many other features.

User documentation is available at http://pilip.lnx.warwick.ac.uk/docs/master/QuimP_Guide.html, developers can check http://pilip.lnx.warwick.ac.uk/site/apidocs/index.html

Citation

Please, make the following citation in any publication related to our software:

"QuimP [1] used in this study was developed at the University of Warwick with support from BBSRC (BBR grant BB/M01150X/1).”

[1] Piotr Baniukiewicz, Sharon Collier, Till Bretschneider, QuimP: analyzing transmembrane signalling in highly deformable cells. Bioinformatics, Volume 34, Issue 15, 1 August 2018, Pages 2695-2697, doi: 10.1093/bioinformatics/bty169.

Registration

Warwick University has introduced new security measures which meant the current registration process is broken.

Please use these credentials until further notice:

Till

Bretschneider

[email protected]

University of Warwick

6acabdc13ec3121d13defddcc8394a11

Build

Clone the repository and update submodules which are required to run tests:

git clone https://github.com/CellDynamics/QuimP.git
git submodule init
git submodule update

Then, use standard Maven approach, e.g.:

mvn package

This will produce QuimP_xxx.jar with program as well as separate jars with source and tests. Note that tests depend on git submodule repository which checks out to nonstandard resource folder.

Javadoc

JavaDoc jar is not built by default. To get it use:

mvn clean com.github.jeluard:plantuml-maven-plugin:generate javadoc:jar 

One can also use the profile build-javadoc provided by pom-scijava-base. This profile builds full Java doc with all direct dependencies attached:

mvn clean package -P build-javadoc -Dproject.build.sourceEncoding=cp1252
# QuimP uses UTF-8 encoding by default but some dependencies use other and build fails. Setting cp1252 partially solves the problem.  

Maven profiles

There are the following profiles defined in QuimP pom and closely related parent poms:

1. installation - default profile, sets location of manual to master branch
2. testing - block registration window
3. development - sets location of manual to develop branch. It uses also mocked BOA filters and blocks registration window.
4. dev-collectdeps - copies all project dependencies to target/dependencies