{"id":19728826,"url":"https://github.com/swharden/prairieview-quick-loader","last_synced_at":"2026-06-09T18:31:21.855Z","repository":{"id":140792300,"uuid":"501436150","full_name":"swharden/PrairieView-Quick-Loader","owner":"swharden","description":"ImageJ plugin to quickly load multiphoton imaging data from PrairieView 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PrairieView Quick Loader\n\n**PrairieView Quick Loader is an ImageJ plugin for quickly loading large PrairieView TSeries folders as 5D hyperstacks.** Image metadata is read from XML using code from the [bioformats](https://github.com/ome/bioformats/blob/master/components/formats-gpl/src/loci/formats/in/PrairieMetadata.java) library, but performance is enhanced by limiting the number of times the filesystem is scanned and XML documents are parsed and interpreted.\n\n\u003cdiv align='center'\u003e\n\u003cimg src='dev/screenshot.png'\u003e\n\u003c/div\u003e\n\n## Installation\n\n* [Stock ImageJ](https://imagej.nih.gov/ij/download.html) (not [Fiji](https://fiji.sc/)) is recommended for performance\n\n* Download the plugin `.jar` from the [Releases page](https://github.com/swharden/ImageJ-QuickPV/releases/) \n\n* Place the `.jar` in ImageJ's `plugins/` folder and restart ImageJ\n\n* Click `Plugins`, `Quick PrairieView Loader`, and select a TSeries XML file\n\n## Benchmark\n\nTime to load a TSeries with 99 sequences of 2-channel 31-slice stacks (6,138 TIFs, 776 MB) from a SSD:\n\n* Bio-Formats Importer: 10 minutes and 17 seconds\n\n* QuickPV: 58 seconds\n\n* Single file TIF: \u003c1 second\n\n## Build from Source\n\n* Get the [JDK](https://www.oracle.com/java/technologies/downloads/)\n\n* Download [Maven](https://maven.apache.org/download.cgi) and extract it somewhere important\n\n* Create `JAVA_HOME` environment variable with value `C:\\Program Files\\Java\\jdk-17.0.2`\n\n* Create `MAVEN_HOME` environment variable with value `C:\\path\\to\\apache-maven-3.8.4`\n\n* Add `C:\\path\\to\\apache-maven-3.8.4\\bin` to your list of system path variables\n\n* Run `mvn -v` to verify Maven is setup correctly\n\n* Run `mvn` in this folder to compile the plugin and put it in `target/`\n\n## Automate Conversion\n\nThe following ImageJ macro can be used to automate loading XML files from a collection of PrairieView folders and save the data as a single file .tif in the References subfolder. This greatly improves loading times over network connections where loading thousands of individual files is extremely slow:\n\n```java\nfunction ProcessFolder(dir, folderName){\n\t\n    // locate the XML file\n    xmlFilePath = dir+folderName+\"/\"+folderName+\".xml\";\n    if (!File.exists(xmlFilePath))\n        exit(\"XML file does not exist:\\n\" + xmlFilePath);\n        \n    // determine output filenames\n    outputTifPath = dir+folderName+\"/References/\"+folderName+\".tif\";\n    outputPngPath = dir+folderName+\"/References/\"+folderName+\"_proj.png\";\n    \n    // check if analysis is required\n    if (File.exists(outputTifPath)){\n    \tprint(\"Skipping (output file exists)\");\n    \treturn;\n    }\n    \n    // load source data\n    print(\"Loading: \" + xmlFilePath);\n    run(\"Quick PrairieView Loader\", \"select=[\" + xmlFilePath + \"]\");\n    \n    // make channel 1 magenta instead of red\n    Stack.setPosition(1,1,1);\n    run(\"Magenta\");\n\t\n    // save the full stack\n    print(\"Saving: \" + outputTifPath);\n\tsaveAs(\"Tiff\", outputTifPath);\n\n    // create and save a projection\n    run(\"Z Project...\", \"projection=[Average Intensity]\");\n    run(\"RGB Color\");\n    print(\"Saving: \" + outputPngPath);\n    saveAs(\"PNG\", outputPngPath);\n}\n\nfunction ProcessSubFolders(dir){\n\tprint(\"\\\\Clear\");\n\tif (!endsWith(dir, \"/\"))\n\t\tdir = dir + \"/\";\n\t\t\n\tif (!File.isDirectory(dir))\n\t    exit(\"Folder not found:\\n\" + dir);\n\t        \n\tlist = getFileList(dir);\n\tfor (i=0; i\u003clist.length; i++) {\n\t    if (!endsWith(list[i], \"/\"))\n\t        continue;\n\t    folderName = list[i].replace(\"/\",\"\");\n\t    \n\t    print(\"\");\n\t    print(\"Processing \" + i + 1 + \" of \" + list.length + \": \" + folderName);\n\t    ProcessFolder(dir, folderName);\n\t\tclose(\"*\");\n\t}\n}\n\nProcessSubFolders(\"C:\\\\folder\\\\containing\\\\tseries\\\\subfolders\");\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fswharden%2Fprairieview-quick-loader","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fswharden%2Fprairieview-quick-loader","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fswharden%2Fprairieview-quick-loader/lists"}