Incenp.org ImageJ Plugins are a set of plugins for the ImageJ image analysis software.

the plugins are distributed under the terms of the GNU General Public License, version 3 or higher.

Available plugins

Currently, the set contains two plugins: Unified Merge, to create merged images from a hyperstack, and Extended Panel, to create a panel from selected frames in a hyperstack.

Those plugins are not intended to build “publication-quality” figures with all the flexibility that one would expect from a figure preparation tool. Rather, they are intended to provide a quick and easy way to generate “good enough” images. As such, many aspects of the generated images are hard-coded in the plugins’ code and cannot be changed by the user without directly modifying said code.

For users looking for a full-featured figure preparation tool, I would personally recommend OMERO.figure, an application for the OMERO server and its OMERO.web client.

Java library

In addition to the plugins, the package also contains a few Java classes that may be used in other ImageJ plugins or scripts. Those classes are under the org.incenp.imagej namespace.

Refer to the API documentation of the library to know what classes are available and what you can do with them.

Notable classes include the BatchReader class, to facilitate batch processing of images listed in a CSV input file, and the ChannelMasker class, to facilitate the creation and manipulation of binary masks.

Setup

From a binary distribution

Binary distributions, in the form of JAR files, are available on the release page of the project.

Simply download the latest JAR file on that page (named incenp-plugins-X.X.Y.jar, where X.Y.X is the latest version) and save it anywhere under the plugins directory of your ImageJ installation.

The plugins will be available upon the next restart of ImageJ under the Plugins>Incenp.org menu. You may also check the plugins were installed correctly by opening the plugins’ “about” dialog under Help>About Plugins...>Incenp.org Plugins....

From source

You may download the source code either from a tarball archive on the release page, or directly from the Git repository:

$ git clone https://git.incenp.org/damien/imagej-plugins.git

The project uses Maven as its build system, so you need to have Maven installed with the mvn command available from the shell. You will then need to install the parent POM by running:

$ mvn dependency:get -DgroupId=org.incenp -DartifactId=incenp-base \
  -Dversion=1.1.0 -Dpackaging=pom \
  -DremoteRepositories=https://mvn.incenp.org/repo/releases

Then, simply run the following command from the source directory:

$ mvn package

This will generate a JAR archive named incenp-plugins-X.Y.Z.jar in the target directory. Install that file in your ImageJ’s plugins directory as described in the previous section.