Open Source Java Library for Image Creation & Processing

Getting Started with ImgLib2

The easiest and recommended way to install ImgLib2 is via GitHub.

go get -u github.com/imglib/imglib2.git 

Creating New Images via Java

The open source Java library ImgLib2 has included support for creating a new image from the scratch with just a couple of lines of Java code. Using the ImgLib2 library, you can create different types of images such as simple images, 3D images, ImgFactory & more. You can also modify images of the existing images with just a couple of lines of code.

        public Example1c()
        {
            // create the ImgFactory based on cells (cellsize = 5x5x5...x5) that will
            // instantiate the Img
            final ImgFactory< FloatType > imgFactory = new CellImgFactory<>( new FloatType(), 5 );
    
            // create an 3d-Img with dimensions 20x30x40 (here cellsize is 5x5x5)Ø
            final Img< FloatType > img1 = imgFactory.create( 20, 30, 40 );
    
            // create another image with the same size. Note that the input provides the size for the new image as it implements the Interval interface
            final Img< FloatType > img2 = imgFactory.create( img1 );
    
            // display both (but they are empty)
            ImageJFunctions.show( img1 );
            ImageJFunctions.show( img2 );
        }

Image Duplication via Java API

The ImgLib2 library has included functionality for image duplication using Java commands. You can easily make a copy of the existing image. You can employ Cursors to achieve this task. You can also use the copy method which is a generic method and the great thing is that it will work on any kind of Type.

	public DuplicateImage() throws ImgIOException
	{
		// open with SCIFIO as a FloatType
		Img< FloatType > img = IO.openImgs( "DrosophilaWing.tif", new FloatType() ).get( 0 );
 
		// copy the image, as it is a generic method it also works with FloatType
		Img< FloatType > duplicate = copyImage( img );
 
		// display the copy
		ImageJFunctions.show( duplicate );
	}
        // Generic, type-agnostic method to create an identical copy of an Img

	public < T extends Type< T > > Img< T > copyImage( final Img< T > input )
	{
		// create a new Image with the same properties
		
		Img< T > output = input.factory().create( input );
 
		// create a cursor for both images
		Cursor< T > cursorInput = input.cursor();
		Cursor< T > cursorOutput = output.cursor();
 
		// iterate over the input
		while ( cursorInput.hasNext())
		{
			// move both cursors forward by one pixel
			cursorInput.fwd();
			cursorOutput.fwd();
 
			// set the value of this pixel of the output image to the same as the input,
			// every Type supports T.set( T type )
			cursorOutput.get().set( cursorInput.get() );
		}
 
		// return the copy
		return output;
	}
 

View Images Partly via Java

The free ImgLib2 library enables software developers to display of only some parts of the image inside their apps via a couple of lines of Java code. Views are very powerful and you can use them to display selected parts of the images, display a rotated view, and few other things. Views can be RandomAccessible, Interval, and can therefore be made Iterable.

Sparse Data Management via Java

The free ImgLib2 library gives software developers the capability to work with sparse data using Java code. The library has provided two interpolation schemes for displaying sparse data. Users can compute a value for every location in space by returning either the value of the closest sample or an interpolated, distance-weighted value of the k nearest neighbors to the sampled location.

        // Working with sparse data

	public SparseExample()
	{
		// the interval in which to create random points
		FinalInterval interval = new FinalInterval( new long[] { 375, 200 } );
 
		// create an IterableRealInterval
		IterableRealInterval< FloatType > realInterval = createRandomPoints( interval, 250 );
 
		// using nearest neighbor search we will be able to return a value an any position in space
		NearestNeighborSearch< FloatType > search =
			new NearestNeighborSearchOnKDTree<>(
				new KDTree<>( realInterval ) );
 
		// make it into RealRandomAccessible using nearest neighbor search
		RealRandomAccessible< FloatType > realRandomAccessible =
			Views.interpolate( search, new NearestNeighborSearchInterpolatorFactory< FloatType >() );
 
		// convert it into a RandomAccessible which can be displayed
		RandomAccessible< FloatType > randomAccessible = Views.raster( realRandomAccessible );
 
		// set the initial interval as area to view
		RandomAccessibleInterval< FloatType > view = Views.interval( randomAccessible, interval );
 
		// display the view
		ImageJFunctions.show( view );
 
		// compute a gauss on it
		Img< FloatType > convolved = new ArrayImgFactory<>( new FloatType() ).create( interval );
 
		Gauss.inFloat( new double[] { 3, 3 }, view, interval, convolved,
			new Point( view.numDimensions() ), convolved.factory() );
 
		// display the view
		ImageJFunctions.show( convolved );
	}