Introduction to ImageJ

Dr. C. SaravananNIT Durgapur

ImageJ

• Wayne Rasband, National Institute of Mental Health, Bethesda, Md. 23rd Sept, 1997.

• Operating System / Platform Independent.• Open Source• Java based• Full set of imaging functions available• Easy to use

Image types

• Supports common and important image formats.

• Acquires image directly from scanners, cameras and other video sources.

• BMP, Tiff, DICOM, GIF, Jpeg, PGM, PNG, etc.

Macros

• A macro is a simple program that automates a series of ImageJ commands.

• The easiest way to create a macro is to record a sequence of commands using the command recorder.

• A macro is saved as a text file (.txt or .ijm extension).

• Any macro file placed in ImageJ/plugins with an .ijm extension will be installed in the Plugins menu.

Macrosrun ("Close All");open();t=getTime();W = getWidth();H = getHeight();b = 0;c = 0;autoCorr = 0; for (j=0; j<H; j++) { for (i=0; i<W; i++) { p = getPixel(i,j); p1 = getPixel(i+1,j); p2 = getPixel(i+2,j); s = p*p1; t = p*p2; b += s; c += t; } }autoCorr = b-c; TotalTime=getTime()-t;wait (1500);print(autoCorr);

Variables

x = 2 ;y = 3 ;result = x * x + y + y ;student = "Amir"write (" Hello " + student);http://imagej.nih.gov/ij/developer/macro/func

tions.htmlhttp://fiji.sc/wiki/index.php/Introduction_into_

Macro_Programming

Colour

open();run("Duplicate...", "title=step-1");run("HSB Stack");setSlice(2);stack = getImageID();run("Duplicate...", "title=threshold");run("Gamma...", "value=0.30");run("Select All");run("Copy");close();selectImage(stack);run("Paste");setSlice(1);run("Duplicate...", "title=bilateral");run("Enhance Contrast", "saturated=0.4");run("Select All");run("Copy");close();selectImage(stack);run("Paste");run("RGB Color");

Histogram

open();getStatistics(area, mean, min, max, std,

histogram);write(area, mean, min, max, std);Plot.create("Histogram", "Value", "Count",

histogram);for (i=0; i<histogram.length; i++) { setResult("Value", i, i); setResult("Count", i, histogram[i]);}run("Enhance Contrast");saveAs("Jpeg");

Plugins

import ij.*;import ij.process.*;import ij.gui.*;import java.awt.*;import ij.plugin.*;import ij.plugin.frame.*;

public class My_Plugin implements PlugIn {

public void run(String arg) {IJ.open();ImagePlus imp = IJ.getImage();IJ.run(imp, "Invert", "");IJ.wait(1000);IJ.run(imp, "Invert", "");

}}

• Adding a new feature to ImageJ can be done writing a script or macro or plugin.

• Scripts and macros are easier to learn and faster to develop.

• Plugins are a dedicated mechanism for extending ImageJ.

• A plugin consists of one or more Java classes living inside a .jar file in plugins.

• All plugin .jar (or .class) files must contain an underscore in their name.

There are two different types of plugins:• Plugins which operate on one image• All other plugins (including plugins which require more

than one input images, or image format loaders)

• A filter plugin looks like this:public class My_Plugin implements PlugInFilter { public int setup(String arg, ImagePlus image) { return DOES_ALL; } public void run(ImageProcessor ip) { // Here is the action }}

• A general plugin looks like this:

public class My_Plugin implements PlugIn { public void run(String arg) { // Here is the action }}Compile and RunThe PlugInFilter interface verifyies that there is an

image and that it is of the correct type, and error handling than the Plugin interface.

Limitations of Plugins

• Plugins can only implement menu entries (in particular, they cannot provide tools in the toolbar)

• Some functions which are easy to call via macros are not available via the public Java API (e.g. Image>Stacks>Plot Z-axis profile...)

• Quicker to write macros.

Class IJ

The class ij.IJ is a convenience class with many static functions. Two of them are particularly useful for debugging:

• // output into the Log window• IJ.log(“Hello, World!”);• • // Show a message window• IJ.showMessage(“Hello, World!”);

Hierarchy of the classes representing an image

Example

• // get the current image• ImagePlus image = WindowManager.getCurrentImage(); • // get one pixel's value (slow)• float value = ip.getf(0, 0);

• // get all type-specific pixels (fast)• // in this example, a ByteProcessor

byte[] pixels = (byte[])ip.getPixels();int w = ip.getWidth(), h = ip.getHeight();for (int j = 0; j < h; j++) for (int i = 0; i < w; i++) { // Java has no unsigned 8-bit data type, so we need to perform Boolean

arithmetics int value = pixels[i + w * j] & 0xff; //treated as unsigned integer ... }

Colorprocessor

• // get all pixels of a ColorProcessorint[] pixels = (int[])ip.getPixels();int w = ip.getWidth(), h = ip.getHeight();for (int j = 0; j < h; j++) for (int i = 0; i < w; i++) { int value = pixels[i + w * j]; // value is a bit-packed RGB value int red = value & 0xff; int green = (value >> 8) & 0xff; int blue = (value >> 16) & 0xff;}

Histogram 16 bit Grayscaleimport ij.*;import ij.plugin.filter.PlugInFilter;import ij.process.*;import ij.measure.*;import java.awt.*;import java.awt.image.*;

/** Generates a tabular histogram of a 16-bit image. */public class SixteenBit_Histogram implements PlugInFilter {

Calibration cal;ImageStatistics stats;

public int setup(String arg, ImagePlus imp) {if (imp!=null) {

cal = imp.getCalibration();stats = imp.getStatistics();

}return DOES_16+NO_CHANGES;

}

public void run(ImageProcessor ip) {display16bitHistogram(ip);

}

void display16bitHistogram(ImageProcessor ip) {int[] hist = ip.getHistogram();StringBuffer sb = new StringBuffer();int min = (int)cal.getRawValue(stats.min);int max = (int)cal.getRawValue(stats.max);for (int i=min; i<=max; i++)

sb.append((int)cal.getCValue(i)+"\t"+hist[i]+"\n");new ij.text.TextWindow("Histogram", "Value\tCount", new String(sb), 300, 400);

}

}