imagej2
[](https://forum.image.sc/tag/imagej) [](https://github.com/imagej/imagej2/actions/workflows/build.yml) [](https://imagesc.zulipchat.com/#narrow/stream/327236-ImageJ2) [](https://gitpod.io/#https://github.com/imagej/imagej2) This is the repository for [ImageJ2](https://imagej.net/software/imagej2), a rewrite of the original [ImageJ](https://imagej.net/software/imagej) for multidimensional image data, with a focus on scientific imaging. Its central goal is to broaden the paradigm of ImageJ beyond the limitations of the original ImageJ application, to support a wider range of multidimensional scientific image data. To ensure backwards compatibility, ImageJ2 has been designed to fully integrate into the original ImageJ user interface. This allows users to keep using ImageJ in familiar ways, while providing the ability to migrate toward more powerful new features as needed. 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](https://imagej.net/software/omero), from within another Java application such as [KNIME](https://imagej.net/software/knime) or [Icy](https://imagej.net/software/icy), or even from Python-based applications such as [CellProfiler](https://imagej.net/software/cellprofiler) and [napari](https://imagej.net/software/napari) via [PyImageJ](https://pypi.org/project/pyimagej). ImageJ2 has an N-dimensional data model driven by the powerful [ImgLib2](https://imagej.net/libs/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 collaborative development process; for details, see the [Contributing](https://imagej.net/contribute/) page. We collaborate with related projects such as [Fiji](https://imagej.net/software/fiji), [SCIFIO](https://imagej.net/software/scifio), [CellProfiler](https://imagej.net/software/cellprofiler), and [OME](https://openmicroscopy.org/), 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](https://scijava.org/). For more details on the project, see the [ImageJ wiki](https://imagej.net/). # LICENSING ImageJ2 is distributed under a [Simplified BSD License](https://en.wikipedia.org/wiki/BSD_licenses); for the full text of the license, see [LICENSE.txt](https://github.com/imagej/imagej2/blob/main/LICENSE.txt). # IMAGEJ2 AS A LIBRARY ## From Java This repository is the main ImageJ2 application, which brings together all of ImageJ2 under the artifact [net.imagej:imagej](https://maven.scijava.org/index.html#nexus-search;gav~net.imagej~imagej~~~~kw,versionexpand). It is the easiest entry point if you are looking to use ImageJ2 as a library from your own software. E.g., in your Maven `pom.xml`: ``` <parent> <groupId>org.scijava</groupId> <artifactId>pom-scijava</artifactId> <version>42.0.0</version> </parent> ... <dependency> <groupId>net.imagej</groupId> <artifactId>imagej</artifactId> </dependency> ``` We recommend inheriting from the [pom-scijava](https://github.com/scijava/pom-scijava) parent, although it is not required. (If you do not, you will need to include the `<version>` of ImageJ2 in your `<dependency>` declaration, and you may be bitten by [this bug in Maven](https://stackoverflow.com/q/45041888/1207769) regarding the versions of ImageJ2's dependencies that you inherit.) ## From other languages * __JavaScript__: Use the [imagej module on npm](https://www.npmjs.com/package/imagej) to call ImageJ2 in-process from node.js code. * __Python__: Use the [PyImageJ module on PyPi](https://pypi.org/project/pyimagej/) to call ImageJ2 in-process from Python code. * __Ruby, R, LLVM and beyond__: Use [GraalVM](https://www.graalvm.org/) to combine ImageJ2 with Truffle-based languages in the same VM, with shared objects and memory on a single VM heap. * __Interprocess__: Use the [ImageJ Server](https://github.com/imagej/imagej-server) to work with ImageJ2 via a RESTful web services API, between processes on the same machine, or between multiple machines. # DEPENDENCIES This component depends on other, lower level components, each of which lives in its own repository: * [ImageJ Common](https://github.com/imagej/imagej-common) * [ImageJ Legacy](https://github.com/imagej/imagej-legacy) * [ImageJ Ops](https://github.com/imagej/imagej-ops) * [ImageJ Updater](https://github.com/imagej/imagej-updater) * [ImgLib2](https://github.com/imglib/imglib) * [SCIFIO](https://github.com/scifio/scifio) * [SciJava Common](https://github.com/scijava/scijava-common) It also includes various "plugin" components at runtime: * [ImageJ Plugins: Commands](https://github.com/imagej/imagej-plugins-commands) * [ImageJ Plugins: Tools](https://github.com/imagej/imagej-plugins-tools) * [ImageJ Plugins: Uploader: SSH](https://github.com/imagej/imagej-plugins-uploader-ssh) * [ImageJ Plugins: Uploader: WebDAV](https://github.com/imagej/imagej-plugins-uploader-webdav) * [ImageJ Scripting](https://github.com/imagej/imagej-scripting) * [SciJava Plugins: Platforms](https://github.com/scijava/scijava-plugins-platforms) * [SciJava Plugins: Text: Markdown](https://github.com/scijava/scijava-plugins-text-markdown) * [SciJava Plugins: Text: Plain](https://github.com/scijava/scijava-plugins-text-plain) See the [pom.xml](pom.xml) for a complete list of dependencies. # BUGS For a list of known issues, see the [GitHub issues](https://github.com/imagej/imagej2/issues). Please report any bugs by following the [instructions online](https://imagej.net/discuss/bugs).