{"id":925,"date":"2023-06-15T09:57:11","date_gmt":"2023-06-15T07:57:11","guid":{"rendered":"https:\/\/paul-regnier.fr\/?page_id=925"},"modified":"2026-04-14T11:35:18","modified_gmt":"2026-04-14T09:35:18","slug":"tutoriel-pupaid","status":"publish","type":"page","link":"https:\/\/paul-regnier.fr\/en_gb\/tutoriel-pupaid\/","title":{"rendered":"PUPAID tutorial"},"content":{"rendered":"

Warning: this tutorial is only available in English, even if you choose the French language at the bottom of the screen. Thank you for your understanding.<\/strong><\/p>\n\n\n\n

PUPAID: Pipeline for Unleashed Processing and Analysis of Immunofluorescence Data<\/strong><\/p>\n\n\n\n

PUPAID<\/code> is a R + ImageJ package allowing to process immunofluorescence data and perform unsupervised analysis on it using a single cell contouring approach.<\/p>\n\n\n

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\"\"\n\t\t\t\n\t\t\t\t\n\t\t\t<\/svg>\n\t\t<\/button>
An AI-generated visual representation of what PUPAID<\/code> could be in real life. Drawn by Craiyon.<\/strong><\/figcaption><\/figure>\n<\/div>\n\n\n

Table of contents<\/strong><\/h2>\n\n\n\n
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  1. Prerequisites<\/a>\n
      \n
    1. R environment introduction and installation<\/a><\/li>\n\n\n\n
    2. PUPAID R package installation<\/a><\/li>\n\n\n\n
    3. Load PUPAID<\/a><\/li>\n\n\n\n
    4. Update PUPAID<\/a><\/li>\n\n\n\n
    5. R Shiny interactive application<\/a><\/li>\n\n\n\n
    6. Example dataset<\/a><\/li>\n<\/ol>\n<\/li>\n\n\n\n
    7. Workspace directory setup<\/a><\/li>\n\n\n\n
    8. Pre-process data (optional)<\/a>\n
        \n
      1. Generate a black tile<\/a><\/li>\n\n\n\n
      2. Get the tile image size<\/a><\/li>\n\n\n\n
      3. Rename and order tiles<\/a><\/li>\n\n\n\n
      4. Stitch tiles<\/a><\/li>\n<\/ol>\n<\/li>\n\n\n\n
      5. Analysis<\/a>\n
          \n
        1. Establish \u03c3 pairs to test<\/a><\/li>\n\n\n\n
        2. Benchmark \u03c3 pairs<\/a><\/li>\n\n\n\n
        3. ROI analysis<\/a><\/li>\n\n\n\n
        4. Transform TSV to XLSX<\/a><\/li>\n\n\n\n
        5. Transform TSV to FCS<\/a><\/li>\n\n\n\n
        6. Visual analysis through conventional cytometry software<\/a><\/li>\n<\/ol>\n<\/li>\n\n\n\n
        7. Citation<\/a><\/li>\n<\/ol>\n\n\n\n

          1) Prerequisites<\/strong><\/h2>\n\n\n\n

          1.1) R environment introduction and installation<\/strong><\/h3>\n\n\n\n

          To make the installation of R programming language and RStudio development software easier for new or beginner users, we highly recommend the following ressource, entitled \u00ab\u00a0YaRrr! The Pirate’s Guide to R\u00a0\u00bb<\/a>. New users should at least read the first (\u00ab\u00a0Preface\u00a0\u00bb) and second (\u00ab\u00a0Getting Started\u00a0\u00bb) sections, as they provide clear and straightforward instructions on how to setup R and RStudio on Windows and MacOS operating systems. These sections will allow users to correctly install PUPAID<\/code> and launch it flawlessly.<\/p>\n\n\n\n

          1.2) PUPAID R package installation<\/strong><\/h3>\n\n\n\n

          PUPAID<\/code> package can be installed with the following command:<\/p>\n\n\n\n

          # The following line can be skipped if the devtools package is already installed\n<\/em>\ninstall.packages(<\/strong>\"devtools\")<\/strong>\n\n# Load the devtools package\n<\/em>\nlibrary(<\/strong>\"devtools\")<\/strong>\n\n# Install PUPAID from GitHub repository\n<\/em>\ndevtools::install_github(<\/strong>\"PaulRegnier\/PUPAID\")<\/strong><\/code><\/pre>\n\n\n\n
          1.3) Load PUPAID<\/strong><\/h3>\n\n\n\n
          To load PUPAID<\/code>, simply enter the following command in the R console:<\/p>\n\n\n\n
          library(<\/strong>\"PUPAID\")<\/strong><\/code><\/pre>\n\n\n\n
          1.4) Update PUPAID<\/strong><\/h3>\n\n\n\n
          To update PUPAID<\/code>, simply enter the following command in the R console:<\/p>\n\n\n\n
          devtools::install_github(<\/strong>\"PaulRegnier\/PUPAID\", force = TRUE)<\/strong><\/code><\/code><\/pre>\n\n\n\n
          1.5) R Shiny interactive application<\/strong><\/h3>\n\n\n\n
          If one is not very familiar with programming and\/or the R environment, PUPAID<\/code> also provides an interactive application which uses the R shiny<\/code> package. Once the package is installed (see previous section), users can launch the Shiny application with the following command:<\/p>\n\n\n\n
          PUPAID::interactivePUPAID()<\/strong><\/code><\/pre>\n\n\n\n
          The process of launching PUPAID<\/code>‘s interactive R Shiny application within RStudio can be visualized in the video below:<\/p>\n\n\n\n