Project
This document describes the properties of the JSON API object. You also can access the document in JSON Schema format: project.schema.json
An analysis project
- jipipe:project-type: string , x ∈ { project (default) }
-
Used to identify this JSON as JIPipe project
- metadata: See metadata [object Object]
-
General information about the project
- dependencies: object[]
-
Dependencies of this project
- graph: See graph [object Object]
-
Contains the pipeline nodes
- compartments: object [object Object]
-
For organization of compartments
- compartment-graph: See graph [object Object]
-
Structural graph of compartments
Example
{
"jipipe:project-type" : "project",
"metadata" : {
"name" : "Empty (3 compartments)",
"description" : "This template contains three compartments 'Preprocessing', 'Analysis', and 'Postprocessing' that are connected to each other.",
"authors" : [ ],
"website" : "",
"license" : "",
"citation" : ""
},
"dependencies" : [ {
"metadata" : {
"name" : "Standard plots",
"description" : "Commonly used plot 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://jipipe.org/",
"license" : "BSD 2-Clause",
"citation" : ""
},
"id" : "org.hkijena.jipipe:plots",
"version" : "1.0.0"
}, {
"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://jipipe.org/",
"license" : "BSD 2-Clause",
"citation" : ""
},
"id" : "org.hkijena.jipipe:imagej-algorithms",
"version" : "1.0.0"
}, {
"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://jipipe.org/",
"license" : "BSD 2-Clause",
"citation" : ""
},
"id" : "org.hkijena.jipipe:filesystem",
"version" : "1.0.0"
}, {
"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://jipipe.org/",
"license" : "BSD 2-Clause",
"citation" : ""
},
"id" : "org.hkijena.jipipe:compartments",
"version" : "1.0.0"
}, {
"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://jipipe.org/",
"license" : "BSD 2-Clause",
"citation" : ""
},
"id" : "org.hkijena.jipipe:imagej-integration",
"version" : "1.0.0"
} ],
"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" : null
}
}
},
"graph" : {
"nodes" : {
"preprocessing-folder-list" : {
"jipipe:slot-configuration" : { },
"jipipe:algorithm-ui-location" : {
"preprocessing" : {
"Vertical" : {
"x" : 400,
"y" : 300
}
}
},
"jipipe:node-info-id" : "import-folder-list",
"jipipe:algorithm-compartment" : "preprocessing",
"jipipe:algorithm:save-outputs" : true,
"jipipe:algorithm:enabled" : true,
"folder-paths" : [ "ATTC_IµL_3rdReplicate-Experiment-5516", "ATTC_IµL_3rdReplicate-Experiment-5517", "ATTC_IµL_3rdReplicate-Experiment-5518" ],
"jipipe:algorithm:pass-through" : false,
"jipipe:node:name" : "Folder list",
"jipipe:node:description" : null
},
"preprocessing-path-to-annotation" : {
"jipipe:slot-configuration" : { },
"jipipe:algorithm-ui-location" : {
"preprocessing" : {
"Vertical" : {
"x" : 400,
"y" : 500
}
}
},
"jipipe:node-info-id" : "path-to-annotation-simple",
"jipipe:algorithm-compartment" : "preprocessing",
"annotation-merge-strategy" : "OverwriteExisting",
"remove-extensions" : true,
"jipipe:algorithm:save-outputs" : true,
"jipipe:algorithm:enabled" : true,
"jipipe:parallelization:enabled" : true,
"generated-annotation" : "Dataset",
"full-path" : false,
"jipipe:algorithm:pass-through" : false,
"jipipe:node:name" : "Path to annotation",
"jipipe:node:description" : null,
"jipipe:parameter-slot-algorithm/has-parameter-slot" : false,
"jipipe:parameter-slot-algorithm/attach-parameter-annotations" : true,
"jipipe:parameter-slot-algorithm/attach-only-non-default-parameter-annotations" : true,
"jipipe:parameter-slot-algorithm/parameter-annotations-prefix" : "",
"jipipe:parameter-slot-algorithm/parameter-annotations-use-internal-names" : false
},
"preprocessing-list-files" : {
"jipipe:slot-configuration" : { },
"jipipe:algorithm-ui-location" : {
"preprocessing" : {
"Vertical" : {
"x" : 425,
"y" : 700
}
}
},
"jipipe:node-info-id" : "folder-list-files",
"jipipe:algorithm-compartment" : "preprocessing",
"jipipe:algorithm:save-outputs" : true,
"jipipe:algorithm:enabled" : true,
"jipipe:parallelization:enabled" : true,
"subfolder" : "in",
"recursive-follows-links" : true,
"filters" : [ {
"mode" : "Glob",
"filter-string" : "*.tif",
"invert" : false
} ],
"only-filenames" : true,
"jipipe:algorithm:pass-through" : false,
"recursive" : false,
"jipipe:node:name" : "List files",
"jipipe:node:description" : null,
"jipipe:parameter-slot-algorithm/has-parameter-slot" : false,
"jipipe:parameter-slot-algorithm/attach-parameter-annotations" : true,
"jipipe:parameter-slot-algorithm/attach-only-non-default-parameter-annotations" : true,
"jipipe:parameter-slot-algorithm/parameter-annotations-prefix" : "",
"jipipe:parameter-slot-algorithm/parameter-annotations-use-internal-names" : false
},
"preprocessing-import-image" : {
"jipipe:slot-configuration" : { },
"jipipe:algorithm-ui-location" : {
"preprocessing" : {
"Vertical" : {
"x" : 425,
"y" : 900
}
}
},
"jipipe:node-info-id" : "import-imagej-imgplus-from-file",
"jipipe:algorithm-compartment" : "preprocessing",
"jipipe:algorithm:save-outputs" : true,
"generated-image-type" : "imagej-imgplus",
"title-annotation" : {
"content" : "Image title",
"enabled" : false
},
"jipipe:algorithm:enabled" : true,
"jipipe:parallelization:enabled" : true,
"jipipe:algorithm:pass-through" : false,
"jipipe:node:name" : "Import image",
"jipipe:node:description" : null,
"jipipe:parameter-slot-algorithm/has-parameter-slot" : false,
"jipipe:parameter-slot-algorithm/attach-parameter-annotations" : true,
"jipipe:parameter-slot-algorithm/attach-only-non-default-parameter-annotations" : true,
"jipipe:parameter-slot-algorithm/parameter-annotations-prefix" : "",
"jipipe:parameter-slot-algorithm/parameter-annotations-use-internal-names" : false
},
"preprocessing-preprocessing-output" : {
"jipipe:slot-configuration" : {
"input" : {
"Data" : {
"slot-data-type" : "imagej-imgplus-2d-greyscale",
"slot-type" : "Input",
"inherited-slot" : null,
"name" : "Data",
"custom-name" : null,
"inheritance-conversions" : { }
}
},
"output" : {
"Data" : {
"slot-data-type" : "imagej-imgplus-2d-greyscale",
"slot-type" : "Output",
"inherited-slot" : null,
"name" : "Data",
"custom-name" : null,
"inheritance-conversions" : { }
}
}
},
"jipipe:algorithm-ui-location" : {
"preprocessing" : {
"Vertical" : {
"x" : 425,
"y" : 1100
}
},
"analysis" : {
"Vertical" : {
"x" : 100,
"y" : 50
}
}
},
"jipipe:node-info-id" : "jipipe:compartment-output",
"jipipe:algorithm-compartment" : "preprocessing",
"jipipe:algorithm:save-outputs" : true,
"jipipe:algorithm:enabled" : true,
"jipipe:algorithm:pass-through" : false,
"jipipe:node:name" : "Preprocessing output",
"jipipe:node:description" : null
},
"analysis-gaussian-blur-2d" : {
"jipipe:slot-configuration" : { },
"jipipe:algorithm-ui-location" : {
"analysis" : {
"Vertical" : {
"x" : 100,
"y" : 250
}
}
},
"jipipe:node-info-id" : "ij1-blur-gaussian2d",
"jipipe:algorithm-compartment" : "analysis",
"jipipe:algorithm:save-outputs" : true,
"jipipe:algorithm:enabled" : true,
"jipipe:parallelization:enabled" : true,
"sigma-y" : -1.0,
"sigma-x" : 1.0,
"jipipe:algorithm:pass-through" : false,
"jipipe:node:name" : "Gaussian blur 2D",
"jipipe:node:description" : null,
"jipipe:parameter-slot-algorithm/has-parameter-slot" : false,
"jipipe:parameter-slot-algorithm/attach-parameter-annotations" : true,
"jipipe:parameter-slot-algorithm/attach-only-non-default-parameter-annotations" : true,
"jipipe:parameter-slot-algorithm/parameter-annotations-prefix" : "",
"jipipe:parameter-slot-algorithm/parameter-annotations-use-internal-names" : false
},
"analysis-auto-threshold-2d" : {
"jipipe:slot-configuration" : { },
"jipipe:algorithm-ui-location" : {
"analysis" : {
"Vertical" : {
"x" : 100,
"y" : 450
}
}
},
"jipipe:node-info-id" : "ij1-threshold-auto2d",
"jipipe:algorithm-compartment" : "analysis",
"jipipe:algorithm:save-outputs" : true,
"jipipe:algorithm:enabled" : true,
"method" : "Default",
"jipipe:parallelization:enabled" : true,
"dark-background" : true,
"jipipe:algorithm:pass-through" : false,
"jipipe:node:name" : "Auto threshold 2D",
"jipipe:node:description" : null,
"jipipe:parameter-slot-algorithm/has-parameter-slot" : false,
"jipipe:parameter-slot-algorithm/attach-parameter-annotations" : true,
"jipipe:parameter-slot-algorithm/attach-only-non-default-parameter-annotations" : true,
"jipipe:parameter-slot-algorithm/parameter-annotations-prefix" : "",
"jipipe:parameter-slot-algorithm/parameter-annotations-use-internal-names" : false
},
"analysis-distance-transform-watershed-2d" : {
"jipipe:slot-configuration" : { },
"jipipe:algorithm-ui-location" : {
"analysis" : {
"Vertical" : {
"x" : 100,
"y" : 650
}
}
},
"jipipe:node-info-id" : "ij1-binary-dtwatershed2d",
"jipipe:algorithm-compartment" : "analysis",
"jipipe:algorithm:save-outputs" : true,
"jipipe:algorithm:enabled" : true,
"jipipe:parallelization:enabled" : true,
"jipipe:algorithm:pass-through" : false,
"jipipe:node:name" : "Distance transform watershed 2D",
"jipipe:node:description" : null,
"jipipe:parameter-slot-algorithm/has-parameter-slot" : false,
"jipipe:parameter-slot-algorithm/attach-parameter-annotations" : true,
"jipipe:parameter-slot-algorithm/attach-only-non-default-parameter-annotations" : true,
"jipipe:parameter-slot-algorithm/parameter-annotations-prefix" : "",
"jipipe:parameter-slot-algorithm/parameter-annotations-use-internal-names" : false
},
"analysis-find-particles-2d" : {
"jipipe:slot-configuration" : { },
"jipipe:algorithm-ui-location" : {
"analysis" : {
"Vertical" : {
"x" : 100,
"y" : 850
}
}
},
"jipipe:node-info-id" : "ij1-analyze-find-particles2d",
"jipipe:algorithm-compartment" : "analysis",
"min-particle-circularity" : 0.0,
"jipipe:algorithm:enabled" : true,
"jipipe:parallelization:enabled" : true,
"jipipe:algorithm:pass-through" : false,
"jipipe:node:name" : "Find particles 2D",
"jipipe:node:description" : null,
"min-particle-size" : 0.0,
"jipipe:algorithm:save-outputs" : true,
"annotation-type" : {
"content" : "Image index",
"enabled" : false
},
"max-particle-circularity" : 1.0,
"split-slices" : true,
"exclude-edges" : false,
"measurements" : {
"values" : [ "Centroid", "PixelValueMinMax", "Area" ]
},
"max-particle-size" : "Infinity",
"jipipe:parameter-slot-algorithm/has-parameter-slot" : false,
"jipipe:parameter-slot-algorithm/attach-parameter-annotations" : true,
"jipipe:parameter-slot-algorithm/attach-only-non-default-parameter-annotations" : true,
"jipipe:parameter-slot-algorithm/parameter-annotations-prefix" : "",
"jipipe:parameter-slot-algorithm/parameter-annotations-use-internal-names" : false
},
"analysis-analysis-output" : {
"jipipe:slot-configuration" : {
"input" : {
"Spore Mask" : {
"slot-data-type" : "imagej-imgplus-2d-greyscale-mask",
"slot-type" : "Input",
"inherited-slot" : null,
"name" : "Spore Mask",
"custom-name" : null,
"inheritance-conversions" : { }
},
"Spore ROI" : {
"slot-data-type" : "imagej-roi",
"slot-type" : "Input",
"inherited-slot" : null,
"name" : "Spore ROI",
"custom-name" : null,
"inheritance-conversions" : { }
},
"Spore measurements" : {
"slot-data-type" : "imagej-results-table",
"slot-type" : "Input",
"inherited-slot" : null,
"name" : "Spore measurements",
"custom-name" : null,
"inheritance-conversions" : { }
}
},
"output" : {
"Spore Mask" : {
"slot-data-type" : "imagej-imgplus-2d-greyscale-mask",
"slot-type" : "Output",
"inherited-slot" : null,
"name" : "Spore Mask",
"custom-name" : null,
"inheritance-conversions" : { }
},
"Spore ROI" : {
"slot-data-type" : "imagej-roi",
"slot-type" : "Output",
"inherited-slot" : null,
"name" : "Spore ROI",
"custom-name" : null,
"inheritance-conversions" : { }
},
"Spore measurements" : {
"slot-data-type" : "imagej-results-table",
"slot-type" : "Output",
"inherited-slot" : null,
"name" : "Spore measurements",
"custom-name" : null,
"inheritance-conversions" : { }
}
}
},
"jipipe:algorithm-ui-location" : {
"postprocessing" : {
"Vertical" : {
"x" : 100,
"y" : 50
}
},
"analysis" : {
"Vertical" : {
"x" : 50,
"y" : 1050
}
}
},
"jipipe:node-info-id" : "jipipe:compartment-output",
"jipipe:algorithm-compartment" : "analysis",
"jipipe:algorithm:save-outputs" : true,
"jipipe:algorithm:enabled" : true,
"jipipe:algorithm:pass-through" : false,
"jipipe:node:name" : "Analysis output",
"jipipe:node:description" : null
},
"postprocessing-plot-tables" : {
"jipipe:slot-configuration" : { },
"jipipe:algorithm-ui-location" : {
"postprocessing" : {
"Vertical" : {
"x" : 550,
"y" : 250
}
}
},
"jipipe:node-info-id" : "plot-from-table",
"jipipe:algorithm-compartment" : "postprocessing",
"plot-type" : "plot-histogram",
"jipipe:algorithm:save-outputs" : true,
"jipipe:algorithm:enabled" : true,
"jipipe:algorithm:pass-through" : false,
"jipipe:node:name" : "Plot tables",
"jipipe:node:description" : null,
"plot-parameters/export-height" : 768,
"plot-parameters/value-axis-label" : "Value",
"plot-parameters/bins" : 10,
"plot-parameters/export-width" : 1024,
"plot-parameters/bin-axis-label" : "Bin",
"plot-parameters/histogram-type" : "Frequency",
"plot-parameters/title" : "Histogram plot",
"column-assignments" : {
"parameters" : {
"Value" : {
"name" : "Value",
"description" : "Values to generate a histogram from. (Numeric column)",
"visibility" : "TransitiveVisible",
"field-class" : "org.hkijena.jipipe.extensions.tables.parameters.TableColumnSourceParameter",
"value" : {
"mode" : "PickColumn",
"column-source" : {
"mode" : "Equals",
"filter-string" : "Area",
"invert" : false
},
"generator-source" : {
"generator-type" : null,
"generated-type" : "NumericColumn"
}
},
"short-key" : "Value",
"ui-order" : 0,
"field-class-id" : "table-column-source"
}
}
}
},
"postprocessing-postprocessing-output" : {
"jipipe:slot-configuration" : {
"input" : { },
"output" : { }
},
"jipipe:algorithm-ui-location" : {
"postprocessing" : {
"Vertical" : {
"x" : 1100,
"y" : 50
}
}
},
"jipipe:node-info-id" : "jipipe:compartment-output",
"jipipe:algorithm-compartment" : "postprocessing",
"jipipe:algorithm:save-outputs" : true,
"jipipe:algorithm:enabled" : true,
"jipipe:algorithm:pass-through" : false,
"jipipe:node:name" : "Postprocessing output",
"jipipe:node:description" : null
}
},
"edges" : [ {
"source-algorithm" : "analysis-analysis-output",
"target-algorithm" : "postprocessing-plot-tables",
"source-slot" : "Spore measurements",
"target-slot" : "Input",
"metadata" : {
"ui-hidden" : false
}
}, {
"source-algorithm" : "preprocessing-import-image",
"target-algorithm" : "preprocessing-preprocessing-output",
"source-slot" : "Image",
"target-slot" : "Data",
"metadata" : {
"ui-hidden" : false
}
}, {
"source-algorithm" : "analysis-gaussian-blur-2d",
"target-algorithm" : "analysis-auto-threshold-2d",
"source-slot" : "Output",
"target-slot" : "Input",
"metadata" : {
"ui-hidden" : false
}
}, {
"source-algorithm" : "analysis-distance-transform-watershed-2d",
"target-algorithm" : "analysis-analysis-output",
"source-slot" : "Output",
"target-slot" : "Spore Mask",
"metadata" : {
"ui-hidden" : true
}
}, {
"source-algorithm" : "preprocessing-list-files",
"target-algorithm" : "preprocessing-import-image",
"source-slot" : "Files",
"target-slot" : "Files",
"metadata" : {
"ui-hidden" : false
}
}, {
"source-algorithm" : "preprocessing-preprocessing-output",
"target-algorithm" : "analysis-gaussian-blur-2d",
"source-slot" : "Data",
"target-slot" : "Input",
"metadata" : {
"ui-hidden" : false
}
}, {
"source-algorithm" : "analysis-distance-transform-watershed-2d",
"target-algorithm" : "analysis-find-particles-2d",
"source-slot" : "Output",
"target-slot" : "Mask",
"metadata" : {
"ui-hidden" : false
}
}, {
"source-algorithm" : "analysis-auto-threshold-2d",
"target-algorithm" : "analysis-distance-transform-watershed-2d",
"source-slot" : "Output",
"target-slot" : "Input",
"metadata" : {
"ui-hidden" : false
}
}, {
"source-algorithm" : "preprocessing-path-to-annotation",
"target-algorithm" : "preprocessing-list-files",
"source-slot" : "Annotated paths",
"target-slot" : "Folders",
"metadata" : {
"ui-hidden" : false
}
}, {
"source-algorithm" : "analysis-find-particles-2d",
"target-algorithm" : "analysis-analysis-output",
"source-slot" : "Measurements",
"target-slot" : "Spore measurements",
"metadata" : {
"ui-hidden" : false
}
}, {
"source-algorithm" : "preprocessing-folder-list",
"target-algorithm" : "preprocessing-path-to-annotation",
"source-slot" : "Folder paths",
"target-slot" : "Paths",
"metadata" : {
"ui-hidden" : false
}
}, {
"source-algorithm" : "analysis-find-particles-2d",
"target-algorithm" : "analysis-analysis-output",
"source-slot" : "ROI",
"target-slot" : "Spore ROI",
"metadata" : {
"ui-hidden" : false
}
} ]
},
"compartments" : {
"compartment-graph" : {
"nodes" : {
"preprocessing" : {
"jipipe:slot-configuration" : {
"input" : { }
},
"jipipe:algorithm-ui-location" : {
"DEFAULT" : {
"Vertical" : {
"x" : 50,
"y" : 50
}
}
},
"jipipe:node-info-id" : "jipipe:project-compartment",
"jipipe:algorithm-compartment" : "DEFAULT",
"jipipe:node:name" : "Preprocessing",
"jipipe:node:description" : null
},
"analysis" : {
"jipipe:slot-configuration" : {
"input" : {
"Preprocessing" : {
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