{ "jipipe:project-type" : "project", "metadata" : { "name" : "Glomeruli segmentation", "description" : "\n \n \n \n \n

\n This project segments the tissue and glomeruli of LSFM slices. It is \n separated into three compartments: \n

\n

\n \n

\n

\n Preprocessing loads the image(s) \n

\n

\n Tissue segments the tissue and extracts the area and other \n measurements \n

\n

\n Glomeruli segments the glomeruli and extracts for each glomerulus \n the centroid, circularity, and other measurements \n

\n

\n \n

\n

\n Edit the Input file parameter on the right-hand side. Point it to \n the input slice. \n

\n

\n \n

\n

\n Run the pipeline by clicking `Run` at the top-right corner. After \n running the pipeline, you will find all final and intermediate results \n in a table. \n

\n

\n \n

\n

\n Exercise \n

\n

\n \n

\n

\n Connect the blocks into a working algorithm that segments the tissue and \n glomeruli. Start with the blocks in `Preprocessing`, as those read all \n the input images. This project contains all necessary algorithm blocks \n to solve the task. You do not need to delete nodes, but feel free to \n play around with other algorithms (e.g. plot generation). Some nodes \n require from you to set up some parameters. The final result will be \n statistics that contain the tissue area and glomeruli measurements. \n Please do not forget the constraints of the glomerular structures: \n

\n

\n \n

\n

\n Minimum radius 15 µm\n

\n

\n Maximum radius 65 µm\n

\n

\n \n

\n

\n Each pixel has a width of 5.1590 µm and a height of 5.1590 \n µm.\n

\n \n\n", "authors" : [ ], "website" : "https://asb-conference.hki-jena.de/event/16/", "license" : "", "citation" : "", "update-site-dependencies" : [ ], "template-description" : "" }, "dependencies" : [ { "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" : [ ] }, { "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" : "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" : [ ] } ], "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" : { 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