ImageJ1-ImageJ2 cheat sheet

This page summarizes translation of basic operations of ImageJ1 and ImageJ2 API. Based on the work of Robert Haase, Scientific Computing Facility, MPI-CBG Dresden.

Task ImageJ1 ImageJ2
Starting ImageJ
new ij.ImageJ();
ImageJ ij = new net.imagej.ImageJ();
ij.ui().showUI();
Show images imp is an ImagePlus object
imp.show()
ij.ui().show(imp);
ImageJFunctions.show(imp);
ImageJFunctions.wrap(imp,"Image").show();
Retrieve an active image object
ImagePlus imp = IJ.getImage();
Script parameter (the same for Dataset, ImagePlus, etc.):
#@ Img image

In Java code:

@Parameter
private Img image;

Using ImageDisplayService:

Dataset image = ij.imageDisplay().getActiveDataset();
Open an image file IJ.openImage() returns an ImagePlus object without showing.
ImagePlus imp = IJ.openImage(urlOrFilePath);
imp.show();

IJ.open() automatically shows the image without returning ImagePlus.

IJ.open(urlOrFilePath);
ImagePlus imp = IJ.getImage();
Using IOService:
Object image = ij.io().open(urlOrFilePath);

Using DatasetIOService (for type safety):

Dataset image = ij.scifio().datasetIO().open(urlOrFilePath);
Save an image file
IJ.saveasTiff(imp, "/path/to/image.tif")
Using IOService:
ij.io().save(dataset, "/path/to/image.tif");

Using DatasetIOService:

ij.scifio().datasetIO().save(dataset, "/path/to/image.tif");
Convert image types Convert from ImageJ2 Img object to ImageJ1 ImagePlus object:
ImagePlus imp = ImageJFunctions.wrap(img,"Title");
Convert from ImageJ1 ImagePlus object to ImgLib2 Img object:
Img<T> realImg = ImageJFunctions.wrapReal(imp);
Img<FloatType> floatImg = ImageJFunctions.convertFloat(imp);
Img<FloatType> realImg2 = ImageJFunctions.wrap(imp);
Show regions
imagePlus.setRoi(roi)
Img<BitType> mask; // = ...
ImagePlus maskImp =ImageJFunctions.wrap(mask, "mask");
// threshold the mask to get an ROI
ImageProcessor imageProcessor = maskImp.getProcessor();
imageProcessor.setThreshold(128,128,ImageProcessor NO_LUT_UPDATE);
Roi roi = new ThresholdToSelection().convert(imageProcessor);
imagePlus.setRoi(roi);
Run plugins
IJ.run(imagePlus,"Normalisation","");
ij.command().run(ImageNormalizerIJ2Plugin.class, true, "input", img, "ij", ij);
Define plugins
public class ImageNormalizerPlugin implements PluginFilter {
  ...
}

In resources/plugins.config:

Plugins>Filtering, "Normalisation", NormalizerPlugin
@Plugin(type = Command.class, menuPath = "Plugins>Normalization")
public class ImageNormalizerIJ2Plugin implements Command {
  ...
}


See also

https://github.com/mpicbg-scicomp/ij2course-images/blob/master/slides/ij_legacy_cheetsheet.pdf