XTensions for ImageJ

bpImarisAdapter (22-08-2008)

The following XTension bpImarisAdapter is a Java™ developed plugin for use with the public domain image processing software called ImageJ (developped by Wayne Rasband).

The plugin allows the exchange of 3D images between Imaris and ImageJ, thus enabling the use of the powerful image processing abilities of ImageJ on Imaris datasets. In addition, 4D datasets can also be processed through the use of dedicated ImageJ macros.

ImageJ 1.31 and Imaris 4.1.3 with valid licenses for Imaris and ImarisXT are required to run the plugin.

• bpImarisAdapter.zip : ImageJ plugin binaries. The file contains jniwrapper library (jniwrap.jar, jniwrap.dll) and runtime license files (jniwrap.lic) as well as the bpImaris_Adapter.jar (V1.0.2), bpImaris_Adapter2.jar (V1.0.3, for Imaris 6.1 and above) and readme.txt file.
• bpImarisAdapter.java : ImageJ plugin source code.

Installation

• Download bpImarisAdapter.zip to your computer and unzip the file in ImageJ root directory (typically C:\Program Files\ImageJ).

• Restart ImageJ and you should see the bpImarisAdapter plugin in ImageJ Plugins menu.

• The files jniwrap.dll and jniwrap.lic should lie in ImageJ root directory and the files jniwrap.jar and bpImaris_Adapter.jar in .../ImageJ/Plugins/bpImarisAdapter directory to be fully functional.

Usage

• Start ImageJ.

• Go to Plugins menu and choose either "bpImaris Adapter" or "Imaris Adapter for Imaris 6.1+" depending on the Imaris version you like to run.

• In bpImaris Adapter choose Start/Stop Imaris.

• Import of a selected 3D Imaris Dataset by clicking on Import Data button.

• Export of the last active 3D ImageJ Dataset by clicking on Export Data button.

• Select and apply a user-defined ImageJ macro on a whole Imaris Dataset by clicking on Start Macro button.

Notes

• This plugin is developed using the Java-COM bridge library called JNIWrapper™, licensed from MIIK®. The provided code generation utility allows to generate usable Java classes out of Imaris' COM interface. These generated Java classes are necessary to compile bpImaris_Adapter.java.

• Java-COM bridges are libraries, which greatly ease the access of COM interfaces to Java programmers. Several different libraries exist such as JNIWrapper™, J-Integra™ and the JACOB project (Open source).