Plugins for ImageJ.
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README.md

Incenp-Plugins - Incenp.org ImageJ Plugins

Incenp-Plugins is a set of plugins for the ImageJ image analysis software.

Available Plugins

The Unified_Merge Plugin

This plugin allows to quickly create a composite image from a hyperstack. The resulting image may contain a panel for each individual channels of the source hyperstack or a single panel showing a colorized merge of all channels, or both.

The Extended_Panel Plugin

This plugin extracts an user-specified selection of frames from a hyperstack and generates a new image containing the selected frames disposed in a array.

Helper Library

Bundled with the plugins is a small library of helper classes for use in other plugins or scripts. Notable classes include BatchReader, to facilitate batch processing of images listed in a CSV input file, and ChannelMasker, to facilitate the creation and manipulation of binary masks. Refer to the package´s [Javadoc] (https://incenp.org/dvlpt/imagej-plugins/apidocs/index.html) for more details.

Installation

To build the plugins with Maven, first install the parent POM from my own repository by running

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

You can then build the plugins by running, from the source directory

$ mvn package

Then copy the generated JAR file (found in the target/ folder) to the plugins folder of your ImageJ installation.

(Pre-compiled JAR files are also available for each release on the releases page for the project.)

Once installed (and after restarting ImageJ if it was already running), the plugins will be available in the Plugins > Incenp.org menu.

Copying

Incenp-Plugins is distributed under the terms of the GNU General Public License, version 3 or higher. The full license is included in the LICENSE file of the source distribution.

Homepage and repository

The project is located at https://incenp.org/dvlpt/imagej-plugins/. The source code is available in a Git repository at https://git.incenp.org/damien/imagej-plugins.