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https://github.com/imagej/imagej2

Open scientific N-dimensional image processing :microscope: :sparkler:
https://github.com/imagej/imagej2

computer-vision image-processing

Last synced: 2 days ago
JSON representation

Open scientific N-dimensional image processing :microscope: :sparkler:

Host: GitHub
URL: https://github.com/imagej/imagej2
Owner: imagej
License: bsd-2-clause
Created: 2012-01-26T18:32:43.000Z (almost 13 years ago)
Default Branch: master
Last Pushed: 2024-10-15T19:40:11.000Z (3 months ago)
Last Synced: 2025-01-02T12:04:00.196Z (9 days ago)
Topics: computer-vision, image-processing
Language: Java
Homepage: https://imagej.net/
Size: 107 MB
Stars: 1,209
Watchers: 93
Forks: 334
Open Issues: 136
Metadata Files:
- Readme: README.md
- License: LICENSE.txt

Awesome Lists containing this project

awesome-biological-image-analysis - ImageJ2 - A Rewrite of ImageJ for multidimensional image data, with a focus on scientific imaging. (General image analysis software)

README

        [![Image.sc Forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftags%2Fimagej.json&query=%24.topic_list.tags.0.topic_count&colorB=brightgreen&suffix=%20topics&logo=data:image/png;base64,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)](https://forum.image.sc/tag/imagej)

[![](https://github.com/imagej/imagej2/actions/workflows/build-main.yml/badge.svg)](https://github.com/imagej/imagej2/actions/workflows/build-main.yml)

[![developer chat](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://imagesc.zulipchat.com/#narrow/stream/327236-ImageJ2)

[![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](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/master/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`:

```

  org.scijava

  pom-scijava

  30.0.0

...

  net.imagej

  imagej

```

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 `` of ImageJ2 in

your `` 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).