RImageJ Vignette Sunil Kumar, Ian Fellows August, 2011 The RImageJ package uses ImageJ through rJava to read and manipulate images from various formats. The purpose of the RImageJ Vignette is to show how to get up and running with RImageJ. For details, including a complete list of classes and functions, consult the manual. Please refer to ImageJ documentation for:  

Class hierarchy Member functions of ImageJ classes

Launching GUI ImageJ GUI can be launced from R/JGR console by creating an object of ImageJ class. This can be done in two ways: 1. If Deducer is loaded, then type deducer() and select “RImageJ” menu and then select “Launch GUI” submenu.

You will be able to see a ImageJ GUI now (similar to one shown in figure 1). It creates a GUI by executing following command:

Now, you can use ImageJ either from GUI or through command line by using “imagej” object. 2. Another method is to create ImageJ through command line by executing the command i.e.

Figure 1

Referencing Objects RImageJ uses reference classes to wrap around java classes, so in case, if we need to deal with java object wrapped by Reference class object then we can easily get or set it by using get() and set() function of RImageJ classes. The get() function returns the java object which the Reference class object is wrapping whereas set() function changes the java object which the Reference class object is wrapping(if it is of same type). For example:

Figure 2

Figure 3

Handling Images In RImageJ we can open both Images as well as Stacks(sequence of images) using IJ$open() function of IJ class.

We can save images by using IJ$save() function of IJ class.

We can save images in other formats by using IJ$saveAs() function of IJ class.

We can check whether the given object is Image object or not by calling is.Image() function.

Exploring Data In RImageJ we can see the pixel values of an Image by calling function imageData().

We can rasterize an Image by using raster.Image() function.

We can create Image from data in RImageJ using as.Image() function.

Figure 4

Image Processing RImageJ provides us all the power which ImageJ have. We can analyse images and process them using the functionlities of ImageJ Classes.

Figure 5 NOTE: We would need to coerce data types before passing them as arguments to java objects.

Plugin Support RImageJ have plugin support, which means we can use ImageJ plugins in R. To install a plugin in RImageJ, call installImageJPlugIn() function by passing path to plugin as argument.

If you have a seprate directory which have ImageJ plugins then you can make RImageJ to use that directory as plugins directory by calling setImageJPlugInPath() function

Now refresh menus in GUI to see the plugins in Plugins menu.