{ "jipipe:project-type" : "project", "metadata" : { "name" : "Empty (3 compartments)", "description" : "

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'", "authors" : [ ], "website" : "", "license" : "", "citation" : "", "update-site-dependencies" : [ ], "template-description" : "Project that contains three compartments (Preprocessing, Analysis, Postprocessing)" }, "dependencies" : [ { "metadata" : { "name" : "ImageJ algorithms", "description" : "Integrates ImageJ algorithms into JIPipe", "authors" : [ { "first-name" : "Zoltán", "last-name" : "Cseresnyés", "affiliations" : "Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany" }, { "first-name" : "Ruman", "last-name" : "Gerst", "affiliations" : "Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany\nFaculty of Biological Sciences, Friedrich-Schiller-University Jena, Germany" } ], "website" : "https://www.jipipe.org/", "license" : "BSD 2-Clause", "citation" : "" }, "id" : "org.hkijena.jipipe:imagej-algorithms", "version" : "2021.4", "ij:update-site-dependencies" : [ ], "ij:update-site-providers" : [ ] }, { "metadata" : { "name" : "ImageJ integration", "description" : "Adds support for commonly used ImageJ data types", "authors" : [ { "first-name" : "Zoltán", "last-name" : "Cseresnyés", "affiliations" : "Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany" }, { "first-name" : "Ruman", "last-name" : "Gerst", "affiliations" : "Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany\nFaculty of Biological Sciences, Friedrich-Schiller-University Jena, Germany" } ], "website" : "https://www.jipipe.org/", "license" : "BSD 2-Clause", "citation" : "" }, "id" : "org.hkijena.jipipe:imagej-integration", "version" : "2021.4", "ij:update-site-dependencies" : [ ], "ij:update-site-providers" : [ ] }, { "metadata" : { "name" : "Compartment management", "description" : "Data types required for graph compartment management", "authors" : [ { "first-name" : "Zoltán", "last-name" : "Cseresnyés", "affiliations" : "Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany" }, { "first-name" : "Ruman", "last-name" : "Gerst", "affiliations" : "Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany\nFaculty of Biological Sciences, Friedrich-Schiller-University Jena, Germany" } ], "website" : "https://www.jipipe.org/", "license" : "BSD 2-Clause", "citation" : "" }, "id" : "org.hkijena.jipipe:compartments", "version" : "2021.4", "ij:update-site-dependencies" : [ ], "ij:update-site-providers" : [ ] }, { "metadata" : { "name" : "Filesystem types and algorithms", "description" : "Data types and algorithms for interacting with files and folders", "authors" : [ { "first-name" : "Zoltán", "last-name" : "Cseresnyés", "affiliations" : "Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany" }, { "first-name" : "Ruman", "last-name" : "Gerst", "affiliations" : "Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany\nFaculty of Biological Sciences, Friedrich-Schiller-University Jena, Germany" } ], "website" : "https://www.jipipe.org/", "license" : "BSD 2-Clause", "citation" : "" }, "id" : "org.hkijena.jipipe:filesystem", "version" : "2021.4", "ij:update-site-dependencies" : [ ], "ij:update-site-providers" : [ ] } ], "additional-metadata" : { "pipeline-parameters" : { "jipipe:type" : "org.hkijena.jipipe.ui.settings.JIPipeProjectInfoParameters", "exported-parameters" : { "parameter-reference-groups" : [ ] } }, "org.hkijena.jipipe:pipeline-parameters" : { "jipipe:type" : "org.hkijena.jipipe.ui.settings.JIPipeProjectInfoParameters", "exported-parameters" : { "parameter-reference-groups" : [ ] } }, "org.hkijena.jipipe.ui:project-tabs" : { "jipipe:type" : "org.hkijena.jipipe.ui.project.JIPipeProjectTabMetadata", "data" : { "open-tabs" : [ "singleton:INTRODUCTION", "singleton:COMPARTMENT_EDITOR", "graph-compartment:preprocessing", "graph-compartment:analysis", "graph-compartment:postprocessing" ], "selected-tab" : "graph-compartment:analysis" } } }, "graph" : { "nodes" : { "preprocessing-input-file" : { "jipipe:slot-configuration" : { "input" : { }, "output" : { "Filenames" : { "slot-data-type" : "file", "slot-type" : "Output", "inherited-slot" : "", "name" : "Filenames", "custom-name" : "blobs.gif", "is-virtual" : false, "save-outputs" : true, "is-optional" : false, "inheritance-conversions" : { } } } }, "jipipe:ui-grid-location" : { "preprocessing" : { "Vertical" : { "x" : 14, "y" : 1 } } }, "jipipe:node-info-id" : "import-file-list", "jipipe:graph-compartment" : "preprocessing", "jipipe:algorithm:enabled" : true, "file-names" : [ "blobs.gif" ], "jipipe:algorithm:pass-through" : false, "jipipe:node:name" : "Input file", "jipipe:node:description" : "" }, "preprocessing-import-image" : { "jipipe:slot-configuration" : { "input" : { "Files" : { "slot-data-type" : "file", "slot-type" : "Input", "inherited-slot" : null, "name" : "Files", "custom-name" : null, "is-virtual" : false, "save-outputs" : true, "is-optional" : false, "inheritance-conversions" : { } } }, "output" : { "Image" : { "slot-data-type" : "imagej-imgplus", "slot-type" : "Output", "inherited-slot" : null, "name" : "Image", "custom-name" : null, "is-virtual" : true, "save-outputs" : true, "is-optional" : false, "inheritance-conversions" : { } } } }, "jipipe:ui-grid-location" : { "preprocessing" : { "Vertical" : { "x" : 14, "y" : 5 } } }, "jipipe:node-info-id" : "import-imagej-imgplus-from-file", "jipipe:graph-compartment" : "preprocessing", "generated-image-type" : "imagej-imgplus", "title-annotation" : { "content" : "Image title", "enabled" : false }, "jipipe:algorithm:enabled" : true, "jipipe:parallelization:enabled" : true, "remove-lut" : true, "jipipe:algorithm:pass-through" : false, "jipipe:node:name" : "Import image", "jipipe:node:description" : "", "jipipe:parameter-slot-algorithm/has-parameter-slot" : false, "jipipe:parameter-slot-algorithm/attach-only-non-default-parameter-annotations" : true, "jipipe:parameter-slot-algorithm/attach-parameter-annotations" : true, "jipipe:parameter-slot-algorithm/parameter-annotations-prefix" : "", "jipipe:parameter-slot-algorithm/parameter-annotations-use-internal-names" : false, "jipipe:data-batch-generation/limit" : { "content" : { "value" : "0-9" }, "enabled" : false } }, "preprocessing-median-blur-2d" : { "jipipe:slot-configuration" : { "input" : { "Input" : { 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