ImageJ

EE4H, M.Sc 0407191Computer VisionDr. Mike Spann

m.spann@bham.ac.ukhttp://www.eee.bham.ac.uk/spannm

Contents

About ImageJImage representation in ImageJDisplaying images in ImageJImageJ utility classRegions of interestWriting plug-ins

About ImageJAll of this material is taken from the

ImageJ tutorial accessed from my web-site

http://mtd.fh-hagenberg.at/depot/imaging/imagej/

Also check out the ImageJ home pagehttp://rsb.info.nih.gov/ij/

ImageJ is a free image processing system allowing easy development of Java based image processing algorithms in the form of plug-ins

About ImageJIt comes with a user-friendly GUI and can

run either as an application or an applethttp://rsb.info.nih.gov/ij/applet/

About ImageJIt can handle 8,16,24 and 32 bit imagesIt can handle most standard image formats

TIFFGIFJPEGBMPDICOM

It can handle stacks of imagesAlso there are plug-ins allowing it to handle

movie filesIt can also handle regions of interest

(ROI’s)

About ImageJThe key point about ImageJ is that it is simple

to add your own algorithms (written as plug-ins) callable from the front-end GUIFile I/O taken care of by ImageJPixel access easy from image handles defined

within ImageJ

Image representation in ImageJImageJ has 5 built-in image classes

8 bit grayscale (byte)8 bit colour (byte)16 bit grayscale (short)RGB colour (int)32 bit image (float)

It also supports image stacks consisting of images (slices) of the same size

Image representation in ImageJImageJ uses 2 classes to represent and

manipulate imagesImagePlus

An image is represented by an ImagePlus objectImageProcessor

This holds the pixel data and contains methods to access the pixel data

Image representation in ImageJPixel access methods in ImageProcessor

includeObject getPixels() – returns a reference to the

pixel array (need to cast to appropriate type)int getHeight() – returns height of pixel arrayint getWidth() – returns width of pixel array

Image representation in ImageJA subclass of ImageProcessor is passed to the

run() method of the plug-in filter (see later) ByteProcessor - 8 bit grayscale images ShortProcessor – 16 bit grayscale imagesColorProcessor – RGB imagesFloatProcessor – 32 bit floating point images

Image representation in ImageJPixel representation in ImageJ uses the byte

datatype for grayscale and colour images and short for 16-bit grayscalebyte/short are signed data types

byte ranges from –128 to 127 short ranges from –32768 to 32767

Obviously grayscale values are usually positive values

Image representation in ImageJTo cast a byte to an integer, we need to

eliminate the sign bit

Can cast back the other way easily enough

byte[] pixels=(byte[]) ip.getPixels();

int grey=0xxff & pixels[j];

pixels[j]=(byte) grey;

Image representation in ImageJThe ColorProcessor return the pixels as int[]

and the RGB values are packed into the one int variable

int[] pixels=(int[]) ip.getPixels();int red=(0xxff0000 & pixels[j]) >> 16;int green=(0xx00ff00 & pixels[j]) >> 8;int blue=(0xx0000ff & pixels[j]);

0 bit31

Image representation in ImageJCan reconstitute an RGB array by shifting the

other way :

pixels[j]=((red & 0xff)<<16)+((green & 0xff)<<8)+(blue & 0xff);

Displaying images in ImageJA class ImageWindow is used to display

ImagePlus objects We don’t normally need to access methods of

ImageWindowThese are automatically called from ImagePlus

methods show(), draw() and updateAndDraw()

ImageJ utility classImageJ contains a class called IJ which

contains a number of useful static methodsError messages

static void error(String message) – displays an error message in a dialog box

static boolean showMessageWithCancel(String title, String message) – allows the user to cancel the plug in or continue

ImageJ utility classDisplaying text

static void write(String s) - Outputs text in a window – useful for displaying textual or numerical results of algorithms

Displaying text in a status barstatic void showStatus(String s)

ImageJ utility classUser input

static double getNumber(String prompt, double default) – Allows the user to input a number in a dialog box

static String getString(String prompt, String default) – Allows the user to input a string in a dialog box

The GenericDialog class is a more sophisticated way of inputting more than a single number or string

Regions of interest (ROI’s)A plug in filter does not always have to

work on the whole imageImageJ supports ROI’s which can are

usually rectangular but can be other shapes as well.

We set/get the ROI using the following method of the ImageProcessor classvoid setROI(int x, int y, int w int h)Rectangle getROI()

Writing plug-insTo write a plug in requires developing a class

which implements either the PlugIn or PlugInFilter interfacesThe second is more usual as this is used when

the filter requires an input image

import ij.*;import ij.plugin.filter.PlugInFilter;import ij.process;

class myPlugin implements PlugInFilter

Writing plug-insMethods setup() and run() must then be

providedMethod setup() sets up the plugin filter for use

String arg allows input arguments to be passed to the plugin

Argument imp handled automatically by ImageJ It’s the currently active image

int setup(String arg, ImagePlus imp)

Writing plug-insMethod setup() returns a flag word

representing the capabilities of the plug-in filter (for example the types of images it can handle). For example :static int DOES_8Gstatic int DOES_RGBstatic int DOES_ALLstatic int NO_CHANGES (plug in doesn’t

change the image data)static int ROI_REQUIREDetc

Writing plug-insThe run() method is called when the plugin is

run from the ImageJ menuIt contains the code to process individual pixels

If no input image is required

If an input image is required

void run(String arg)

void run(ImageProcessor ip)

Writing plug-insOnce the Java program is written and

compiled, the .class file is stored in the plug-in directory which is a sub-directory of the ImageJ home directoryThe class name should contain an underscore

symbol (eg MyAlgorithm_ )It then appears under the plug-in sub-menu of

the ImageJ gui

Conclusions ImageJ is a useful and flexible environment

for developing Java-based image processing algorithms

User algorithms can be simply added to a GUI using the concept of a plug-in

ImageJ allows easy access to image pixel data for a range of image types