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https://github.com/CellDynamics/QuimP
QuimP is software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane.
https://github.com/CellDynamics/QuimP
cell imagej motility segmentation
Last synced: 29 days ago
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QuimP is software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane.
- Host: GitHub
- URL: https://github.com/CellDynamics/QuimP
- Owner: CellDynamics
- License: other
- Created: 2017-01-24T11:12:50.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2023-11-27T23:11:00.000Z (about 1 year ago)
- Last Synced: 2024-08-04T00:12:54.692Z (4 months ago)
- Topics: cell, imagej, motility, segmentation
- Language: Java
- Homepage: http://www.warwick.ac.uk/quimp
- Size: 36.2 MB
- Stars: 6
- Watchers: 5
- Forks: 1
- Open Issues: 33
-
Metadata Files:
- Readme: Readme.md
- Changelog: CHANGELOG.md
- License: LICENSE.txt
Awesome Lists containing this project
- awesome-biological-image-analysis - QuimP - Software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane. (Cell migration and particle tracking)
README
[](http://search.maven.org/#search%7Cga%7C1%7Cg%3A%22com.github.celldynamics.quimp%22%20AND%20a%3A%22QuimP_%22)
# 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](http://pilip.lnx.warwick.ac.uk/docs/master/QuimP_Guide.html), developers can check [http://pilip.lnx.warwick.ac.uk/site/apidocs/index.html](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](https://academic.oup.com/bioinformatics/article/34/15/2695/4939330). *Bioinformatics*, Volume 34, Issue 15, 1 August 2018, Pages 2695-2697, [doi: 10.1093/bioinformatics/bty169](https://doi.org/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
University of Warwick
6acabdc13ec3121d13defddcc8394a11
# Build
Clone the repository and update submodules which are required to run tests:
```bash
git clone https://github.com/CellDynamics/QuimP.git
git submodule init
git submodule update
```
Then, use standard Maven approach, e.g.:
```bash
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:
```bash
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:
```bash
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`