murphycd / imagej

Open source scientific multidimensional image processing

ImageJ2 is a new version of ImageJ seeking to strengthen both the software and its community. Internally, it is a total redesign of ImageJ, but it is backwards compatible with ImageJ 1.x via a "legacy layer" and features a user interface closely modeled after the original.

Under the hood, ImageJ2 completely isolates the image processing logic from the graphical user interface (UI), allowing ImageJ2 commands to be used in many contexts, including headless in the cloud or on a server such as OMERO, or from within another application such as KNIME, Icy or CellProfiler (a Python application).

ImageJ2 has an N-dimensional data model driven by the powerful ImgLib2 library, which supports image data expressed in an extensible set of numeric and non-numeric types, and accessed from an extensible set of data sources. ImageJ2 is driven by a state-of-the-art, collaborative development process, including version control, unit testing, automated builds via a continuous integration system, a bug tracker and more.

We are collaborating closely with related projects including Fiji, SCIFIO and OME, and are striving to deliver a coherent software stack reusable throughout the life sciences community and beyond. For more details, see the SciJava web site.

ImageJ2 is currently in the "beta" stage, meaning the code is not finished. It is being released for early community feedback and testing. Comments, questions and bug reports are much appreciated!

To maintain ImageJ's continuity of development, we have modeled the application after ImageJ v1.x as much as is reasonable. However, please be aware that ImageJ2 is essentially a total rewrite of ImageJ from the ground up. It provides backward compatibility with older versions of ImageJ by bundling the latest v1.x code and translating between "legacy" and "modern" image structures.

For more details on the project, see the ImageJ web site.

LICENSING

ImageJ2 is distributed under a Simplified BSD License; for the full text of the license, see LICENSE.txt.

For the list of developers and contributors, see the parent POM.

IMAGEJ AS A LIBRARY

This repository is the master ImageJ application, which brings together all of ImageJ under the artifact net.imagej:imagej. It is the easiest entry point if you are looking to use ImageJ as a library from your own software. E.g., in your Maven pom.xml:

<parent>
  <groupId>net.imagej</groupId>
  <artifactId>pom-imagej</artifactId>
  <version>2.35</version>
</parent>
...
<dependency>
  <groupId>net.imagej</groupId>
  <artifactId>imagej</artifactId>
</dependency>

We recommend inheriting from the pom-imagej parent, although it is not required. (If you do not, you will need to include the <version> of ImageJ in your <dependency> declaration.)

DEPENDENCIES

This component depends on other, lower level components, each of which lives in its own repository:

• ImageJ Common
• ImageJ Legacy
• ImageJ OPS
• ImageJ Updater
• ImgLib2
• SCIFIO
• SciJava Common

It also includes various "plugin" components at runtime:

• ImageJ Plugins: Commands
• ImageJ Plugins: Tools
• ImageJ Plugins: Uploader: SSH
• ImageJ Plugins: Uploader: WebDAV
• SciJava Plugins: Platforms
• SciJava Plugins: Text: Markdown
• SciJava Plugins: Text: Plain
• Scripting: Beanshell
• Scripting: Clojure
• Scripting: Java
• Scripting: JavaScript
• Scripting: JRuby
• Scripting: Jython

See the pom.xml for a complete list of dependencies.

BUGS

For a list of known issues, see the GitHub issues.

Please report any bugs by following the instructions online.