https://github.com/swharden/prairieview-quick-loader

ImageJ plugin to quickly load multiphoton imaging data from PrairieView folders
https://github.com/swharden/prairieview-quick-loader

fluorescence fluorescence-microscopy-imaging imagej imagej-plugin microscopy multiphoton

Last synced: about 2 months ago
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ImageJ plugin to quickly load multiphoton imaging data from PrairieView folders

• Host: GitHub
• URL: https://github.com/swharden/prairieview-quick-loader
• Owner: swharden
• License: mit
• Created: 2022-06-08T23:01:48.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2023-09-11T19:29:06.000Z (over 1 year ago)
• Last Synced: 2024-05-29T17:16:41.840Z (7 months ago)
• Topics: fluorescence, fluorescence-microscopy-imaging, imagej, imagej-plugin, microscopy, multiphoton
• Language: Java
• Homepage:
• Size: 66.4 KB
• Stars: 0
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# PrairieView Quick Loader

**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.







## Installation

* [Stock ImageJ](https://imagej.nih.gov/ij/download.html) (not [Fiji](https://fiji.sc/)) is recommended for performance

* Download the plugin `.jar` from the [Releases page](https://github.com/swharden/ImageJ-QuickPV/releases/) 

* Place the `.jar` in ImageJ's `plugins/` folder and restart ImageJ

* Click `Plugins`, `Quick PrairieView Loader`, and select a TSeries XML file

## Benchmark

Time to load a TSeries with 99 sequences of 2-channel 31-slice stacks (6,138 TIFs, 776 MB) from a SSD:

* Bio-Formats Importer: 10 minutes and 17 seconds

* QuickPV: 58 seconds

* Single file TIF: <1 second

## Build from Source

* Get the [JDK](https://www.oracle.com/java/technologies/downloads/)

* Download [Maven](https://maven.apache.org/download.cgi) and extract it somewhere important

* Create `JAVA_HOME` environment variable with value `C:\Program Files\Java\jdk-17.0.2`

* Create `MAVEN_HOME` environment variable with value `C:\path\to\apache-maven-3.8.4`

* Add `C:\path\to\apache-maven-3.8.4\bin` to your list of system path variables

* Run `mvn -v` to verify Maven is setup correctly

* Run `mvn` in this folder to compile the plugin and put it in `target/`

## Automate Conversion

The 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:

```java

function ProcessFolder(dir, folderName){

	

    // locate the XML file

    xmlFilePath = dir+folderName+"/"+folderName+".xml";

    if (!File.exists(xmlFilePath))

        exit("XML file does not exist:\n" + xmlFilePath);

        

    // determine output filenames

    outputTifPath = dir+folderName+"/References/"+folderName+".tif";

    outputPngPath = dir+folderName+"/References/"+folderName+"_proj.png";

    

    // check if analysis is required

    if (File.exists(outputTifPath)){

    	print("Skipping (output file exists)");

    	return;

    }

    

    // load source data

    print("Loading: " + xmlFilePath);

    run("Quick PrairieView Loader", "select=[" + xmlFilePath + "]");

    

    // make channel 1 magenta instead of red

    Stack.setPosition(1,1,1);

    run("Magenta");

	

    // save the full stack

    print("Saving: " + outputTifPath);

	saveAs("Tiff", outputTifPath);

    // create and save a projection

    run("Z Project...", "projection=[Average Intensity]");

    run("RGB Color");

    print("Saving: " + outputPngPath);

    saveAs("PNG", outputPngPath);

}

function ProcessSubFolders(dir){

	print("\\Clear");

	if (!endsWith(dir, "/"))

		dir = dir + "/";

		

	if (!File.isDirectory(dir))

	    exit("Folder not found:\n" + dir);

	        

	list = getFileList(dir);

	for (i=0; i