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.
For more details on the project, see the ImageJ web site.
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
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
<parent> <groupId>org.scijava</groupId> <artifactId>pom-scijava</artifactId> <version>16.2.0</version> </parent> ... <dependency> <groupId>net.imagej</groupId> <artifactId>imagej</artifactId> </dependency>
We recommend inheriting from the
pom-scijava parent, although it is not
required. (If you do not, you will need to include the
<version> of ImageJ in
From other languages
- Python: Use the imagej module on pypi to call ImageJ in-process or interprocess from Python code.
- Ruby, R, LLVM and beyond: Use GraalVM to combine ImageJ with Truffle-based languages in the same VM, with shared objects and memory on a single VM heap.
- Interprocess: Use the ImageJ Server to work with ImageJ via a RESTful web services API, between processes on the same machine, or between multiple machines.
This component depends on other, lower level components, each of which lives in its own repository:
It also includes various "plugin" components at runtime:
- ImageJ Plugins: Commands
- ImageJ Plugins: Tools
- ImageJ Plugins: Uploader: SSH
- ImageJ Plugins: Uploader: WebDAV
- ImageJ Scripting
- SciJava Plugins: Platforms
- SciJava Plugins: Text: Markdown
- SciJava Plugins: Text: Plain
See the pom.xml for a complete list of dependencies.
For a list of known issues, see the GitHub issues.
Please report any bugs by following the instructions online.