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JIPipe pipeline projects

JIPipe organizes pipelines in projects that can be saved and loaded from disk. Each pipeline is organized into Compartments that separate the whole graph into functional units. You can find an overview of all compartments\nin the Compartments tab. You can re-open the tab by selecting Compartment > Edit compartments if you closed the tab.

By double-clicking a compartment in the overview, JIPipe will open an editor where you can modify the sub-pipeline\nthat is associated to the compartment. If you just want to run a project, you can find the `Run` button at the top-right\ncorner.\n\nPipeline developers might have organized a set of most common pipeline parameters. You can find them in Project > Project overview\nalongside additional information like the authors, citations, and website.\n\nThis template contains one graph node called 'Analysis'", "summary" : "", "authors" : [ ], "acknowledgements" : [ ], "website" : "", "license" : "", "citation" : "", "dependency-citations" : [ ], "thumbnail" : { "data" : null }, "categories" : [ ], "update-site-dependencies" : [ ], "template-description" : "Project that contains one compartment", "permissions" : { "prevent-adding-deleting-nodes" : false, "prevent-modifying-slots" : false }, "node-templates" : [ ], "restore-tabs" : true }, "dependencies" : [ { "metadata" : { "name" : "Core", "description" : "A JIPipe project", "summary" : "", "authors" : [ ], "acknowledgements" : [ ], "website" : "", "license" : "", "citation" : "", "dependency-citations" : [ ], "thumbnail" : { "data" : null }, "categories" : [ ] }, "id" : "org.hkijena.jipipe:core", "version" : "1.80.0", "ij:update-site-dependencies" : [ ], "dependencies" : [ ], "ij:update-site-providers" : [ ] }, { "metadata" : { "name" : "3D ImageJ Suite integration", "description" : "A JIPipe project", "summary" : "", "authors" : [ ], "acknowledgements" : [ ], "website" : "", "license" : "", "citation" : "", "dependency-citations" : [ ], "thumbnail" : { "data" : null }, "categories" : [ ] }, "id" : "org.hkijena.jipipe:ij-3d", "version" : "1.80.0", "ij:update-site-dependencies" : [ ], "dependencies" : [ ], "ij:update-site-providers" : [ ] }, { "metadata" : { "name" : "Strings", "description" : "A JIPipe project", "summary" : "", "authors" : [ ], "acknowledgements" : [ ], "website" : "", "license" : "", "citation" : "", "dependency-citations" : [ ], "thumbnail" : { "data" : null }, "categories" : [ ] }, "id" : "org.hkijena.jipipe:strings", "version" : "1.80.0", "ij:update-site-dependencies" : [ ], "dependencies" : [ ], "ij:update-site-providers" : [ ] }, { "metadata" : { "name" : "Forms", "description" : "A JIPipe project", "summary" : "", "authors" : [ ], "acknowledgements" : [ ], "website" : "", "license" : "", "citation" : "", "dependency-citations" : [ ], "thumbnail" : { "data" : null }, "categories" : [ ] }, "id" : "org.hkijena.jipipe:forms", "version" : "1.80.0", "ij:update-site-dependencies" : [ ], "dependencies" : [ ], "ij:update-site-providers" : [ ] }, { "metadata" : { "name" : "Compartment management", "description" : "Data types required for graph compartment management", "summary" : "Data types required for graph compartment management", "authors" : [ { "title" : null, "first-name" : "Zoltán", "last-name" : "Cseresnyés", "affiliations-list" : [ "Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany" ], "website" : "https://www.leibniz-hki.de/en/staff-details.html?member=144", "contact" : "zoltan.cseresnyes@leibniz-hki.de", "first-author" : true, "corresponding-author" : false, "custom-text" : "" }, { "title" : null, "first-name" : "Ruman", "last-name" : "Gerst", "affiliations-list" : [ "Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany", "Faculty of Biological Sciences, Friedrich Schiller University Jena, Germany" ], "website" : "https://www.leibniz-hki.de/en/staff-details.html?member=1027", "contact" : "ruman.gerst@leibniz-hki.de", "first-author" : true, "corresponding-author" : false, "custom-text" : "" }, { "title" : null, "first-name" : "Marc Thilo", "last-name" : "Figge", "affiliations-list" : [ "Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany", "Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Germany" ], "website" : "https://www.leibniz-hki.de/en/staff-details.html?member=81", "contact" : "thilo.figge@leibniz-hki.de", "first-author" : false, "corresponding-author" : true, "custom-text" : "" } ], "acknowledgements" : [ ], "website" : "https://www.jipipe.org/", "license" : "BSD 2-Clause", "citation" : "Gerst, R., Cseresnyés, Z. & Figge, M.T. JIPipe: visual batch processing for ImageJ. 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"title" : null, "first-name" : "Curtis T.", "last-name" : "Rueden", "affiliations-list" : [ "Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA" ], "website" : "", "contact" : "", "first-author" : true, "corresponding-author" : false, "custom-text" : "" }, { "title" : null, "first-name" : "Johannes", "last-name" : "Schindelin", "affiliations-list" : [ "Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA", "Morgridge Institute for Research, Madison, Wisconsin, USA" ], "website" : "", "contact" : "", "first-author" : false, "corresponding-author" : false, "custom-text" : "" }, { "title" : null, "first-name" : "Mark C.", "last-name" : "Hiner", "affiliations-list" : [ "Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA" ], "website" : "", "contact" : "", "first-author" : false, "corresponding-author" : false, "custom-text" : "" }, { "title" : null, "first-name" : "Barry E.", "last-name" : "DeZonia", "affiliations-list" : [ "Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA" ], "website" : "", "contact" : "", "first-author" : false, "corresponding-author" : false, "custom-text" : "" }, { "title" : null, "first-name" : "Alison E.", "last-name" : "Walter", "affiliations-list" : [ "Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA", "Morgridge Institute for Research, Madison, Wisconsin, USA" ], "website" : "", "contact" : "", "first-author" : false, "corresponding-author" : false, "custom-text" : "" }, { "title" : null, "first-name" : "Ellen T.", "last-name" : "Arena", "affiliations-list" : [ "Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA", "Morgridge Institute for Research, Madison, Wisconsin, USA" ], "website" : "", "contact" : "", "first-author" : false, "corresponding-author" : false, "custom-text" : "" }, { "title" : null, "first-name" : "Kevin W.", "last-name" : "Eliceiri", "affiliations-list" : [ "Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA", "Morgridge Institute for Research, Madison, Wisconsin, USA" ], "website" : "", "contact" : "", "first-author" : true, "corresponding-author" : true, "custom-text" : "" }, { "title" : null, "first-name" : "Caroline A.", "last-name" : "Schneider", "affiliations-list" : [ "Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA" ], "website" : "", "contact" : "", "first-author" : true, "corresponding-author" : false, "custom-text" : "" }, { "title" : null, "first-name" : "Wayne S.", "last-name" : "Rasband", "affiliations-list" : [ "Section on 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