ImageJ Ivussnakes plugin
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Written by Administrator   
Sunday, 16 August 2009 20:27

Download

To download the .jar file with the source files, you can access the following link.

Install

This is a tool to be used inside ImageJ.

These installation instructions have been tried with ImageJ 1.41o

To install it, extract the jar (using your favorite extractor) to the folder “ImageJ/plugins/Tools”

Notice that the CONTENTS of the .jar must be in the directory “ImageJ/plugins/Tools” and not “ImageJ/plugins/Tools/LiveWire/”.

So, you will see the plugins in places like “ImageJ/plugins/Tools/LiveWire1DTool_.class”.

Then, you need to install the LiveWire buttons through a macro.

This is simple. Start ImageJ then, go to “Plugins→Macro>Install…”. Point to the extracted file: “ImageJ/plugins/Tools/LiveWire.txt”. This will install the LiveWire buttons to ImageJ toolbar.

How to use

After you have installed, you'll be able to use the LiveWire tool. Click on the part of the image you want to start selecting and wait a couple seconds. The LiveWire selection will automatically follow your mouse. When you are ready with the next point, click it and keep going. Right click to finish segmentation.

If you wanna start a new LiveWire, just finish the current one with the right-click and start a new one with the left-click.
To move existing points or add new points after you have finished the selection, hold shift and click the handles or click outside them to add new points.

 

Common Problems

One common error message is due to the wrong version of Java:

 

java.lang.UnsupportedClassVersionError: Bad version number in .class file
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(Unknown Source)
at java.lang.ClassLoader.defineClass(Unknown Source)
at ij.io.PluginClassLoader.loadClass(PluginClassLoader.java:248)
at ij.io.PluginClassLoader.loadClass(PluginClassLoader.java:211)
at ij.IJ.runUserPlugIn(IJ.java:173)
at ij.IJ.runPlugIn(IJ.java:142)
at ij.Executer.runCommand(Executer.java:121)
at ij.Executer.run(Executer.java:58)
at ij.IJ.run(IJ.java:240)
at ij.macro.Functions.doRun(Functions.java:551)
at ij.macro.Functions.doFunction(Functions.java:74)
at ij.macro.Interpreter.doStatement(Interpreter.java:200)
at ij.macro.Interpreter.doBlock(Interpreter.java:511)
at ij.macro.Interpreter.runMacro(Interpreter.java:127)
at ij.macro.MacroRunner.run(MacroRunner.java:126)
at java.lang.Thread.run(Unknown Source)

 

Or something like:

java.lang.UnsupportedClassVersionError: Bad version number in .class file

at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(Unknown Source)
at java.security.SecureClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.access$100(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at ij.IJ.runUserPlugIn(IJ.java:177)
at ij.IJ.runPlugIn(IJ.java:146)
at ij.Executer.runCommand(Executer.java:122)
at ij.Executer.run(Executer.java:59)
at ij.IJ.run(IJ.java:244)
at ij.macro.Functions.doRun(Functions.java:551)
at ij.macro.Functions.doFunction(Functions.java:74)
at ij.macro.Interpreter.doStatement(Interpreter.java:200)
at ij.macro.Interpreter.doBlock(Interpreter.java:512)
at ij.macro.Interpreter.runMacro(Interpreter.java:127)
at ij.macro.MacroRunner.run(MacroRunner.java:126)
at java.lang.Thread.run(Unknown Source)

Please, upgrade your java version to 1.6, known as 6, and these errors will be gone. http://www.java.com/en/download/manual.jsp
If you are sure you are with the right Java version, try updating your ImageJ. Some versions come with Java installed and they might be old Java versions.

FAQ

Can I make multiple selections with LiveWire?
Sure. But you will need to use the ROI Manager.

Go to Analyze -> Tools -> ROI Manager

Make your selection. Click the Add[t] button of ROI Manager (you can just type t if you want). Now create another selection and click the Add button again.
You can click the Show All to see them all, click the Measure to see some data as well save the selections.


Last Updated on Friday, 02 October 2009 20:59
 
IVUS Plugin has been released

In order to make the graduation thesis fully repeatable, I'm making the IVUS plugin available. This ImageJ plugin adds the functionality to slice an image frame sequence in 4 directions, so that longitudinal segmentation may be applied. It is used for Coronary Intravascular ultrasound images.
The download is available here http://sourceforge.net/projects/ivussnakes/files/ under the ivussnakes package in IVUS Plugin release.
Enjoy it!

 
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