{"id":13716994,"url":"https://github.com/CellDynamics/QuimP","last_synced_at":"2025-05-07T06:31:57.143Z","repository":{"id":57719637,"uuid":"79904460","full_name":"CellDynamics/QuimP","owner":"CellDynamics","description":"QuimP is software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane.","archived":false,"fork":false,"pushed_at":"2023-11-27T23:11:00.000Z","size":37926,"stargazers_count":7,"open_issues_count":33,"forks_count":1,"subscribers_count":5,"default_branch":"master","last_synced_at":"2024-11-14T05:33:46.484Z","etag":null,"topics":["cell","imagej","motility","segmentation"],"latest_commit_sha":null,"homepage":"http://www.warwick.ac.uk/quimp","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/CellDynamics.png","metadata":{"files":{"readme":"Readme.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null}},"created_at":"2017-01-24T11:12:50.000Z","updated_at":"2024-09-20T12:10:58.000Z","dependencies_parsed_at":"2024-01-05T23:46:27.122Z","dependency_job_id":"1594c604-b9ce-4596-a983-658c87de510b","html_url":"https://github.com/CellDynamics/QuimP","commit_stats":{"total_commits":1643,"total_committers":5,"mean_commits":328.6,"dds":"0.010346926354230068","last_synced_commit":"50de79f2ec39fee513a75f9732acad0e3765e0ae"},"previous_names":[],"tags_count":60,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CellDynamics%2FQuimP","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CellDynamics%2FQuimP/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CellDynamics%2FQuimP/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CellDynamics%2FQuimP/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CellDynamics","download_url":"https://codeload.github.com/CellDynamics/QuimP/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252826898,"owners_count":21810200,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cell","imagej","motility","segmentation"],"created_at":"2024-08-03T00:01:16.464Z","updated_at":"2025-05-07T06:31:52.129Z","avatar_url":"https://github.com/CellDynamics.png","language":"Java","funding_links":[],"categories":["Cell migration and particle tracking"],"sub_categories":[],"readme":"[![Maven Central](https://img.shields.io/maven-central/v/com.github.celldynamics.quimp/QuimP_.svg)](http://search.maven.org/#search%7Cga%7C1%7Cg%3A%22com.github.celldynamics.quimp%22%20AND%20a%3A%22QuimP_%22)\n\n# About\n\nQuimP software, a set of plugins for ImageJ, has been developed by Till Bretschneider, Richard \nTyson and Piotr Baniukiewicz (current developer) to quantify spatio-temporal patterns of fluorescently labeled proteins in the cortex of moving \ncells.\n\nQuimP was first described in Dormann et al., 2002. For information on the classic version, now \ncalled QuimP1, please follow this link.\n\nQuimP2 which was developed in collaboration with Leonard Bosgraaf (Bosgraaf et al., 2009) \nintroduced a new method to correlate local cortical fluorescence with membrane movement. An \nobsolete QuimP2 installation package can be downloaded here (Unzip the archive and move the contents\nof the two folders according to their directory name. The help icon that appears when launching the\nQuimP toolbar provides an in depth explanation of how to use the associated plugins and the \nindividual parameters). An addon for pseudopod analysis resulted in QuimP3 which however is not \nofficially supported by the main QuimP development team (contact Leonard Bosgraaf for help instead).\n\nQuimP3 is currently under development. It supports user plugins, other segmentation \nalgorithms, image pre-processing and offers many other features. \n\nUser 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)\n\n## Citation\n\nPlease, make the following citation in any publication related to our software:\n\n\"QuimP [1] used in this study was developed at the University of Warwick with support from BBSRC (BBR grant BB/M01150X/1).”\n\n[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).\n\n\n# Registration\n\nWarwick University has introduced new security measures which meant the current registration process is broken.\n\nPlease use these credentials until further notice:\n\nTill\n\nBretschneider\n\nt.bretschneider@warwick.ac.uk\n\nUniversity of Warwick\n\n6acabdc13ec3121d13defddcc8394a11\n\n\n# Build\n\nClone the repository and update submodules which are required to run tests:\n\n```bash\ngit clone https://github.com/CellDynamics/QuimP.git\ngit submodule init\ngit submodule update\n```\n\nThen, use standard Maven approach, e.g.:\n\n```bash\nmvn package\n```\n\nThis 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.\n\n## Javadoc\n\nJavaDoc jar is not built by default. To get it use:\n\n```bash\nmvn clean com.github.jeluard:plantuml-maven-plugin:generate javadoc:jar \n```\n\nOne can also use the profile `build-javadoc` provided by *pom-scijava-base*. This profile builds full Java doc with all direct dependencies attached:\n\n```bash\nmvn clean package -P build-javadoc -Dproject.build.sourceEncoding=cp1252\n# QuimP uses UTF-8 encoding by default but some dependencies use other and build fails. Setting cp1252 partially solves the problem.  \n```\n\n## Maven profiles\n\nThere are the following profiles defined in QuimP pom and closely related parent poms:\n\n1. *installation* - **default** profile, sets location of manual to `master` branch\n2. *testing* - block registration window\n3. *development* - sets location of manual to `develop` branch. It uses also mocked BOA filters and blocks registration window.\n4. *dev-collectdeps* - copies all project dependencies to `target/dependencies`\n \n\n \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FCellDynamics%2FQuimP","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FCellDynamics%2FQuimP","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FCellDynamics%2FQuimP/lists"}