bigdataviewer-headless

Run ExportImagePlusPlugin in headless mode.

Getting started

1. Install

git clone [email protected]:elephant-track/bigdataviewer-headless.git

cd bigdataviewer-headless
mvn clean package

Please replace $FIJI_HOME depending on your environment.

cp target/bigdataviewer-headless-0.0.1-SNAPSHOT.jar $FIJI_HOME/jars

2. Prepare an ImageJ macro (e.g. Groovy)

import java.io.File
import java.nio.file.Files
import java.nio.file.Path

import ij.IJ
import ij.Macro
import ij.macro.Interpreter
import ij.WindowManager
import org.elephant.bdv.ij.ExportImagePlusPluginHeadless


def main() {
    def tempDir = Files.createTempDirectory( null )
    WindowManager.setTempCurrentImage( IJ.createImage( "Stack", "8-bit", 16, 16, 1, 8, 2 ) )
    Macro.setOptions( "export_path=" + tempDir.toString() + File.separator + "tmp.xml" )
    new ExportImagePlusPluginHeadless().run()
    // Clean up
    tempDir.toFile().eachFileRecurse( File::delete )
    Files.delete( tempDir )
}

main()

You can find an example of converting a data set in Cell Tracking Challenge format to BDV format.

3. Run a macro in headless mode

(Windows)

ImageJ-win64.exe --ij2 --headless --console --run example.groovy

(macOSX)

ImageJ-macosx --ij2 --headless --console --run example.groovy

(Linux)

ImageJ-linux64 --ij2 --headless --console --run example.groovy