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Editing the ImageJ Wiki

This site requires JavaScript to be enabled. Jdk.java.net is where Oracle’s OpenJDK builds are published for download, openjdk.java.net is the OpenJDK project itself. Red Hat It also has an IcedTea project that builds OpenJDK and adds some features.

This page lists answers to the most frequently asked questions.

• 1Usage
• 2Mac OS X
• 3Running
  • 3.1How do I launch ImageJ with a different version of Java?
• 4Installing/Updating
• 5Compatibility
• 6Fiji
• 7Interoperability
• 8Development
• 9Community
• 10Miscellaneous

How do I apply an operation or macro to multiple images?

See the Batch Processing page.

What is the largest size image that ImageJ can open?

There is a 2 gigapixel limit when opening and displaying image planes using the ImageJ 1.x user interface's default image viewer. However, one major goal of the ImageJ2 project is to break this limit. ImageJ2 uses the ImgLib2 library as its data model, which has much larger limits on the number of pixels (theoretically: ~2^63 per dimension, up to ~2^31 dimensions, totaling ~2^63^31 pixels). Hence, you can open larger images using the ImageJ2 API. But you will not be able to display them in the user interface yet.

Furthermore, the SCIFIO library (what ImageJ2 uses for data I/O) supports opening such images on-demand as 'cell images' such that blocks are read from disk as you iterate over the image. This is similar to (but more powerful than) ImageJ 1.x's virtual stacks feature. In this way, you can write code to process these large images without displaying them.

The Fiji project also includes the BigDataViewer (BDV) plugin, which currently functions as an alternative viewer, to display arbitrarily large images backed by ImgLib2. In the future we hope to integrate BDV-driven UI technology more completely into ImageJ core. But there are a couple of limitations right now:

1. BDV was originally designed for large SPIM data; opening large image files more generally currently requires some coding. But we want to change this.
2. Many ImageJ 1.x plugins assume the data is stored in an ImageJ 1.x data structure, which is not what BDV uses. So 'mixing and matching' IJ1 and IJ2 functionality is tricky here. But we are working to lift these restrictions as time goes on.

How do I set up Java 6 on OS X?

See the MacOS page.

How do I run ImageJ on Yosemite?

See the MacOS page.

How do I run ImageJ on El Capitan?

See the MacOS page.

How do I launch ImageJ with a different version of Java?

On Windows

Install Java 8, and delete or rename the ImageJ.appjava and/or ImageJ.appjre folders, if they exist. If this does not result in ImageJ using the expected Java version, check the Environment Variables ( Control Panel › System and Security › System › Advanced Settings › Advanced › Environment Variables) for the variable 'JAVA_HOME'. Update or create this variable as needed; its value should be the desired JDK or JRE that you would like to use for ImageJ (for instance: 'C:Program FilesJavajdk1.8.0_172'). See also Java environment variable setup.

On OS X

Use the --java-home command line option:

Note: the --java-home flag does not support Apple Java installations. Specifying Apple Javas with this flag will give an error message about being unable to find lib/server/libjvm.dylib. However, ImageJ will fall back to Apple Java if no other Java installations are available.

In particular, this means that to run Java 6 on the latest macOS versions, you must do ONE of the following:

• EITHER: Remove all installations of Java 7 and Java 8 (remove the JRE and remove all JDKs).
• OR: Launch ImageJ explicitly using java. Here is a sample invocation for Fiji (copy and paste into Terminal):

See 'How do I setup a launcher app' below for instructions on turning this invocation into a Dock icon.

On Linux

Use the --java-home command line option:

One downside of doing this is that ImageJ will launch in a separate process, which has some unintuitive side effects. For example, Ubuntu's Unity user interface will not allow you to 'Pin to Launcher' in this case...

How do I setup a launcher app for OS X for running with a different JVM version?

Start Automator and select to create an Application. Double-click Run Shell Script in the Library/Utilities folder and replace the text content — cat — with the following:

Save anywhere you like.

To replace this application's icon, Get Info on your real Fiji, click on the icon on the top left, press Cmd-C, Get Info on your Fiji Automator app, click the icon, and press Cmd-V.

You will then see two icons in the dock, the one of the launcher app and the one of Fiji when it's running.

(based on this guide)

What is this headless mode and what do I need it for?

The term headless refers to running ImageJ without a graphical desktop, e.g. on a cluster. See the Headless page for more information.

How can I verify that my ImageJ is really 100% up to date?

ImageJ will report itself as 'up to date' as long as all files installed in your ImageJ match the latest versions from the remote update sites. However, there are cases where your ImageJ may report itself as 'up to date' but still be missing critical files, or have mismatching versions (e.g., the dreaded NoSuchMethodError).

To be certain, run Help › Update..., and click the 'Advanced mode' button. Then verify the following View Options:

• View uninstalled files only: Shows files that are available from remote ImageJ update sites, but not installed in your ImageJ. Consider changing the 'Status/Action' to 'Install' for these items, especially any .jar files that are flagged with 'Not installed' status.
• View locally modified files only: Shows files that have been edited locally (i.e., do not match any version from the remote update sites). Consider changing the 'Status/Action' to 'Update' for these items, especially any .jar files that you did not intentionally modify.
• View local-only files: Shows files that are not known at all to the remote update sites. These files were likely added manually (e.g., if you installed additional plugins manually; see 'How do I install additional plugins' below). Consider deleting these files if you do not need them, especially any .jar files of unknown origin or conflicting file names.

If you flag any changes to be made, press the 'Apply changes' to update your ImageJ. And after restarting ImageJ, you might want to run Help › Update... again to make sure everything looks the way you expect!

How do I install additional plugins?

If the plugin is published on an ImageJ update site, you can run Help › Update then click the Manage update sites button to enable it. Not only does this install the plugins for you automatically, but you will also be notified of any updates whenever they are released.

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Otherwise, you can drag 'n drop the .jar files onto the ImageJ window, or use Plugins › Install Plugin... with .jar, .class and .java files, or copy the plugins to ImageJ.app/plugins/ and restart ImageJ. See the walk-through with screenshots.

How do I downgrade ImageJ?

Downgrading is generally not recommended as a long-term solution, but can be handy to avoid new bugs that crop up.

If you need to downgrade to avoid a critical bug, please report that bug to the developers so that it can be fixed in a future version!

• You can change the version of ImageJ 1.x used via the Help › Update ImageJ... menu item. This only changes the version of ImageJ 1.x—not all ImageJ components, plugins, etc.
• You can switch to a different version of Java.
• You can download a Fiji Life-Line version.

Lastly, if you have not yet upgraded, and have a currently working configuration, you can make a backup copy of your ImageJ folder before upgrading. Then if the upgrade has undesirable consequences, switch back to the old copy.

My plugin runs fine in the Script Editor, but it does not show up in the menus when I install it. What's wrong?

To be picked up as a plugin, the .jar's file name must contain an underscore, and it either needs to contain an appropriate plugins.config file or the class name needs to contain an underscore, too.

The safest way to ensure these conventions is to use the File › Export as .jar file menu item.

I tried to update ImageJ via Help › Update, but it throws an exception instead?

Please download a fresh copy from here.

I updated ImageJ via Help › Update, and now it does not start anymore!

See If ImageJ does not start up on the Troubleshooting page.

The Updater always says Connection refused. Maybe it does not use the proxy?

Indeed, an earlier version of the Updater does not use your system-wide network proxy settings. You can download a new ImageJ to receive the fix. Or you can update the Updater manually like this:

• open the Script Editor with File › New › Script
• set the language to BeanShell in the Language menu of the editor
• paste the following code (and adjust it to match your settings):

• run the script via the Run menu

What is the difference between ImageJ1 and ImageJ2?

ImageJ1 is an extensible platform for scientific image analysis. ImageJ2 is redesigned from the ground up to meet the same needs, yet engineered with future-proof flexibility to adapt to researchers' growing requirements (new data types, higher dimensionality, huge images, etc...).

Will ImageJ1 macros, plugins and scripts still work in ImageJ2?

Yes. We are completely committed to 100% backwards compatibility with ImageJ1. ImageJ2 includes the latest version of ImageJ1 'under the hood' so that existing macros, plugins and scripts will still run the same as before.

ImageJ2 user interfaces are just plugins; ImageJ2 runs with the 'ImageJ1 legacy UI' by default. But we have also created a new ImageJ2 user interface modeled after ImageJ1 to a very large extent, with all the same shortcut keys and behaviors whenever possible. Either way, ImageJ2 looks and feels like ImageJ1, but with a powerful new infrastructure allowing it to process a wider variety of image data more quickly and easily.

Does ImageJ2 support the ImageJ macro language? Is it deprecated?

Thanks to the ImageJ legacy layer, ImageJ1macros will run unchanged in ImageJ2, while also allowing to harness ImageJ2's new parameterized scripting paradigm—something that was previously not possible with the macro language.

The ImageJ1 macro language has been extremely useful to many users. However, it has a substantial limitation: its functions are separate from those available from Java and the other scripting languages.

In ImageJ2, the goal is to provide one unified set of functions, which is fully accessible from Java and all scripting languages. Hence, ImageJ2 plugins and scripts are more flexible than ImageJ1plugins and macros. They can run headless on a server, and are accessible from various applications such as CellProfiler, KNIME, OMERO, and headless from the command line. We would encourage newly developed scripts and plugins to use the ImageJ2 API since it offers these advantages, but the ImageJ1 API will remain accessible, too.

Can I call ImageJ1 API from an ImageJ2 command?

Yes, although it is not recommended. You will lose most of the advantages of ImageJ2 if you embed calls to ImageJ1 within your command. ImageJ1 is rather tightly coupled to AWT and hence does not work well headless. For details, see the Headless page.

Can I call ImageJ2 API from an ImageJ1 plugin?

Yes, see the call-modern-from-legacy tutorial example.

How do I find equivalent commands between ImageJ1 and ImageJ2 API?

ImageJ1-ImageJ2 cheat sheet is available.

What is the difference between Fiji and ImageJ?

Fiji is a distribution of ImageJ: it bundles the core ImageJ application with a curated selection of plugins pre-installed. Specifically, those plugins found on the Fiji update site.

How do I install Fiji?

The installation of Fiji is described on specific pages for MacOSX, Windows and Linux.

How do I turn my ImageJ installation into a Fiji one?

Fiji is just ImageJ. If you are running ImageJ2, simply run Help › Update, click Manage update sites, and enable the Fiji update site.

Or if you are running ImageJ1, you can bootstrap the updater by drag 'n dropping this link onto your running ImageJ and run the Javascript that was opened in a text window. After that, you can run Fiji/ImageJ using the ImageJ launcher that was installed into the ImageJ directory.

How do I develop Fiji in Eclipse?

Please refer to the page Developing Fiji in Eclipse.

How can I build Fiji from the command-line?

Download and build it. You need Git for that (if you are on Windows, please use Git for Windows).

How do I install a Fiji plugin into vanilla ImageJ 1.x?

Doing this is not recommended:

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• Fiji plugin authors test their plugins in Fiji, not vanilla ImageJ 1.x.
• An increasing number of plugins use features of ImageJ2, which are not available in ImageJ 1.x.
• If you install multiple plugins with complex dependency chains in this manner, you may have dependency version conflicts. For things to work, you will need to ensure that all the library versions are compatible. The Fiji maintainers have already solved this problem for the Fiji distribution.

So you could save yourself a lot of pain by using Fiji instead.

That said, you can install a Fiji plugin in a vanilla ImageJ 1.x installation, as long as you copy all its dependencies with it. You can do this as follows:

Then copy target/dependency/*.jar into your ImageJ installation.

You will need Git and Maven installed for this to work.

How can I call ImageJ from MATLAB, or vice versa?

Use the ImageJ-MATLAB update site. See the MATLAB page for details.

Why do I get a NoSuchMethodError/NoSuchClassDefFoundError when running a rebuilt plugin?

This is most likely caused by version skew, i.e. when an incompatible version of a build dependency is installed. Example: if you build against mpicbg-1.0.0.jar and run that plugin in a Fiji which has only installed mpicbg-0.6.1.jar, the latter might miss some methods or classes, or even contain incompatible class definitions.

To investigate, you can use mvn dependency:copy-dependencies on the command-line (to copy all build dependencies into target/dependency/) and then use your favorite Zip tool to look for the class name mentioned in the exception. In Eclipse, you can simply use Ctrl+Shift+T (or Command+Shift+T on MacOSX) to look open the respective class; If a recent enough Eclipse is used, and the default settings have not been tampered with, this will start downloading and show the source attached to the dependency.

Once you know which dependency is supposed to contain the class/method, compare the version number of the file(s) in ImageJ.app/plugins/ and ImageJ.app/jars/.

Sometimes, classes are contained in multiple .jar files. This is a frequent source of problems e.g. when some developers try to be helpful and include dependencies' classes into their plugin .jar files. This is a problem because those class files are naturally not updated when the dependency is installed as a proper, separate .jar file and updated. To investigate such issues, use the Find Jar For Class command in Fiji, to determine which .jar file serves the class you are looking for.

What is Maven, and why did you pick it?

Maven is a system to build .jar files from source code, and to manage dependencies (i.e. it is easy to specify which minimal version of, say, ImageJ is required by the source code).

We picked it because we need a standard way to interact and collaborate with other projects and with each other. For starters, it allows developers to stay with their favorite development environment (Eclipse, Netbeans, IntelliJ, etc).

For details, please refer to our page on Maven.

What is MiniMaven and why did you create it?

Please refer to the MiniMaven and Supported Compilers pages for an explanation.

How do I create a new ImageJ plugin using Maven?

Please refer to our page on Maven.

How do I upload a new release of an ImageJ plugin?

Please refer to the Uploading plugins tutorial.

How do I upload a new release of a core ImageJ library such as ImgLib?

The same way you do a plugin. But it will upload to the ImageJ update site (you can only upload to one update site at a time, though, see also this ticket).

What is the recommended way to develop in ImageJ?

Over the years we evolved a development style as follows:

• create a topic branch
• test as much as you need to be comfortable to merge
• merge
• deal with any fall-out

This development style has been adopted by the ImageJ team, with two additions (making the fall-out step much smaller):

• tests are added as automated regression tests (to be run by the continuous integration whenever new changes were pushed) whenever possible.
• merges are usually done with --no-ff, so that even fast-forwarding branches (i.e. rebased on top of master) will get a merge commit in which the branch is described more broadly.

See also coding style.

Class loading issue in 3-rd party libraries (e.g. JPPF)

Libraries trying to load resources or classes with the current thread's class loader rather than with IJ's class loader may fail. The solution is to first set the current thread's class loader to the IJ-classloader. This must be done from the same thread that will later call the problematic code:

How do I see the source code for a command?

ImageJ is open source; as such, it is possible to inspect the source code for any command, in the interest of transparency and reproducibility.

Here are several ways to do so:

1. Using search.imagej.net
   • Go to http://search.imagej.net/
   • Type in your search
   • Click the GitHub button!
2. Using the Command Finder:
   • Press L for the Command Finder.
   • Type the name of the command.
   • Press ↓ to select it.
   • Click the Source button.
   • This will open the source from the ImageJ web site online source.
   • Note: this method is very convenient, but only works for core ImageJ 1.x sources (e.g., not ImageJ2 code, not Fiji code, etc.).
3. Using GitHub:
   • Using the Command Finder, locate your command, taking note of the Class column's value.
     • E.g., if we type 'make binary' we see that the class is ij.plugin.Thresholder.
   • Open the relevant project in GitHub:
     • E.g., for 'ij.' classes, go to: https://github.com/imagej/ImageJA
   • Press the T key, and type the name of the file you are looking for.
     • In the example above, this is Thresholder.java.
   • You should end up with a hit like: https://github.com/imagej/ImageJA/blob/master/src/main/java/ij/plugin/Thresholder.java.
   • This method requires that you know in which repository the code lives. However, you can combine it with search.imagej.net method above to figure out which repository, then load the code on GitHub, if desired.
4. Using the 'Open Source for Menu Item' command:
   • Run Plugins › Scripting › Open Source for Menu Item.
     • Unfortunately, you must select this from the menu, not using the Command Finder.
   • Run the command whose source you want to see.
     • E.g., Process › Binary › Make Binary.
     • Again, select it from the menu directly, not using the Command Finder.
   • This will open the source using the fiji.sc gitweb interface.

In the future, we plan to make this easier by having one single easy command for viewing the source code.

What are 'external' plugins?

As far as users are concerned, external Fiji plugins are exactly the same as internal Fiji plugins. For developers, 'external plugin' simply implies that the plugin's source code is maintained in its own source code repository. For example, TrakEM2 has been an external Fiji plugin since Fiji's inception.

Where should I put the jars of my plugin?

If you develop a Fiji plugin, the result will be in the form of one or more jars containing your plugin and possibly third-party libraries that you rely on. To deploy your plugin you put the jars in the plugins/ or jars/ Fiji subdirectories. The general idea is that only the jars directly containing plugin classes go into plugins/. Auxiliary and third-party jars go into jars/. (see this mail for more background on this.)

How can I call ImageJ from my software?

If your software is written in Java, we recommend using Maven to structure your project. You can then add dependencies to portions of ImageJ that are of interest to you. See the ImageJ tutorials for examples.

If your software is written in another language such as C or Python, there are many ways to integrate Java functionality. You must choose which one is best for your particular requirements.

To facilitate some use cases, we provide a script for generating a combined bundle of all ImageJ-related JARs in a single uber-JAR library. To use, check out the ImageJ source code and execute:

mvn -Pdeps package

For convenience, we provide a build of this combined JAR file (with suffix -all) from the latest DEVELOPMENT, UNSTABLE version of ImageJ. This build includes the latest changes on the master branch of the source repository. It has not been thoroughly tested and may contain new bugs.

In some cases, use of this JAR file is appropriate and convenient; for example, CellProfiler uses it to integrate with ImageJ. However, you should consider carefully what would be best for your project; see the Uber-JAR page for further information.

Does ImageJ work on mobile devices such as Android?

Not yet as an end-user application. But since Android is a Java-based platform, there is hope. One of the ImageJ2 project's central design goals was a better separation of concerns, which could make things like an Android version of ImageJ possible. In particular, the core components of ImageJ2 are militant in their avoidance of certain Java SE packages not present in the Android version of Java (which is based on Java ME), such as Java AWT.

That said, ImageJ2 has not even been compile-tested yet using an Android SDK, so there are surely many problems which would need to be resolved. In the future, the ImageJ development team hopes to set up some continuous integration surrounding Android. If you are interested in helping drive this effort forward, please see the Android tag on the ImageJ forum!

Another possibility for the future is a client/server version of ImageJ that runs in a web browser using HTML5 and JavaScript, which could include cross-platform support for mobile devices (Android, iPhone, tablets, etc.). Again, much groundwork has been done to make the ImageJ2 core design compatible with such an application, but no one has written the server- or client-side yet. If you are seriously interested in helping to pursue such an application, you might also want to check out the OMERO project, which is a client/server application which has some integration with ImageJ.

Why is there Fiji when there is already ImageJ? And what is this ImageJ2 about?

The ImageJ, Fiji and ImageJ2 projects are very closely related. See ImageJ#Flavors for a thorough breakdown of the differences.

See also:

In short: we all collaborate, but have slightly different focus, hence the different projects and names.

How can we be sure that ImageJ1, ImageJ2 and Fiji aren't going to diverge or fork over time?

We are working to create an architecture where the programs work together and preserve compatibility. Fiji is just ImageJ with batteries included, and ImageJ2 includes ImageJ1 as-is for maximum compatibility. Fiji now uses ImageJ2 at its core. Most importantly, all involved developers are strongly dedicated to avoiding divergence—we are working closely together to ensure that ImageJ2 represents a continuation of ImageJ and Fiji, rather than a project fork.

Would it make sense to merge the ImageJ2 and Fiji projects?

Fiji and ImageJ2 are fundamentally the same software, using the same launcher. So from the standpoint of development effort, the ImageJ2 and Fiji projects have indeed merged. ImageJ2 is the core software, and several pieces of infrastructure originally developed for Fiji have now migrated to ImageJ2 (e.g., the Updater, Launcher and Script Editor components). At heart, Fiji is just a big collection of life sciences plugins (though 'Fijabcolsp' doesn't have quite the same ring to it). In other words, Fiji is just an ImageJ update site ('Fijaius')—and as such, you can obtain a working Fiji installation by downloading ImageJ2, running the updater, and enabling the Fiji update site.

All of that said, we do not want to get rid of the two distinct project names, since people are familiar with both. But we are integrating resources when feasible: e.g., the ImageJ wiki and the Fiji wiki are really both the same wiki with different skins, to make cross-linking more seamless. But we want to ensure it is clear that ImageJ is not a life-sciences-specific project, whereas Fiji is. Historically, because Fiji has a life sciences focus, there have been some users who refused to switch from vanilla ImageJ1 to Fiji even though Fiji makes users' lives easier in lots of ways. With ImageJ2, we want to avoid such misconceptions.

More effort is still needed to clarify web resources, to explain concisely and clearly where people should go in different circumstances. We also have plans to make bug reporting simpler and easier across the projects.

This is a Wiki but I cannot edit it! Why?

If you create an account, you will be able to make edits while logged in.

The Wiki is lacking documentation about X, Y and Z

Please feel free to enhance the Wiki! We are thankful for all contributions!

How do I find more information about Command X?

The first place to check is this wiki. The Fiji's Menu page is especially helpful as it includes links to all the menu commands that ship as part of Fiji.

If documentation is missing for the command you're interested in, you can always view the source directly:

1. Open the Command Finder (Shortcut: L)
2. Filter to the command you're interested in.
3. The `File` column will tell you the plugin where the desired command is contained.
4. You can then use this information to find the source code on GitHub - for core ImageJ or Fiji plugins.
5. From the appropriate project on GitHub, you can find the repository corresponding to the desired plugin.
6. Finally, you can search for the actual file for the command of interest (Shortcut: T).

As a complete example, if you were interested in the 2D Histogram command:

• The Command Finder indicates it's located in VIB.jar
• VIB is a Fiji plugin, so we go to the VIB repository.
• On GitHub, press T, search for 'Histogram', and find the Histogram 2D source.

I have a problem that is not covered on this page!

If you have an issue that is not mentioned here, you might want to ask on one of the mailing lists, or via IRC, or enter a bug report.

How to report issues?

Use the Help › Report a Bug command, which adds a ticket report to the Fiji bug tracker. While private mail might seem more desirable sometimes, but it is almost always inferior to the open process we established in ImageJ. For starters, bug reporters are unlikely to know who would be the best person to address the issue.

I reported an issue, but it is still not fixed! Why not?

ImageJ is an Open Source community project. The list of contributors is large but most of the people involved are not paid to work on it. We greatly value community contributions and assistance.

There are not many professional developers whose formal jobs include responding to and addressing bug reports. These developers are not paid solely to fix bugs—rather, they are working to solve scientific problems and to advance the software's capabilities. And their attention is spread thin across many projects: ImageJ, Fiji, SCIFIO, SciJava, LOCI, OME, ImgLib2, OpenSPIM, SLIM Curve, NAR plugin for Maven, and others.

The organizations above total over 300 source code repositories, many of which have dozens of open issues in their issue trackers. There are also several hundred tickets in the old ImageJ issue tracker that are pending migration to GitHub Issues, as well as over a hundred open issues in the Fiji Bugzilla.

So please understand that just because we have not responded to a bug report, does not mean we are uninterested in fixing it. It's just that we are very busy, and can use all the help we can get!

If you want to increase the chances of your issue being worked on, you can:

• Report the issue using the Report a Bug plugin (in the Help menu).
• Provide a minimal, complete, verifiable example.
• Describe what you already tried.
• Put as much effort into your question as you expect to be put into its response.
• Consider debugging the issue yourself and submitting a fix as a pull request.

See the bug reporting best practices article for details.

How do I contribute a bug fix or patch, or propose an idea for a change?

See the Contributing page!

Why do you program in Java? Is C++ not much faster?

See the Philosophy page!

With Oracle buying Sun and Apple deprecating Java, does Java have a future?

Yes. Java is one of the most popular programming languages and still one of the top choices for high-performance, cross-platform applications. Oracle is unlikely to attempt to 'kill' Java, but even if they tried they probably couldn't—OpenJDK is open source and there is a massive community of Java developers behind it. Now that Apple is partnering with Oracle and the OpenJDK community, we are likely to see Java on macOS get better, not worse. Java's popularity will eventually wane, but not because of any company's actions now. Rather, as with any programming language, new technologies will emerge and gain popularity, over a course of many years.

Why does ImageJ still target Java 6?

As of June 2014, around 19% of macOS systems still run version 10.6 Snow Leopard or older [1]. (In December 2013, it was around 25%.) Unfortunately, Apple and the OpenJDK developer community decided to target OS X 10.7 Lion and above for Java 7 and 8. For the time being, to avoid abandoning older machines which cannot be upgraded from Snow Leopard, ImageJ continues to target Java 6.

Furthermore, updating the required version to a newer version of Java would necessitate improvements to the ImageJ Updater such that it could also update the bundled version of Java, which would be a substantial undertaking. Otherwise, most existing installations of ImageJ would stop working, and those users would need to download ImageJ from scratch again.

See this mailing list thread for further details.

How are you addressing the fact that with increased modularity comes increased complexity?

See the Philosophy page!

How about a version of ImageJ for the web browser, mobile devices, etc.?

While a pure web version of ImageJ would be desirable for a number of reasons, there are several substantial challenges with current technology. In particular, it would be difficult for a Javascript-based ImageJ to maintain compatibility with existing plugins, macros and scripts. For now, our goal is to continue improving the Java version of ImageJ, while remaining cognizant of developments in the web applications domain, to reduce the difficulties of a web version at some future date.

We are developing ImageJ with a careful eye toward modularity, avoiding gratuitous dependencies—particularly on AWT, which is not available on most mobile devices. We hope this approach makes it easier to port ImageJ to additional platforms in the future.

A shorter term pragmatic solution would be an ImageJ web client that connects to a remote server running ImageJ in headless mode, which does the heavy lifting. See also the OMERO project.

Why is open software vital to science?

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See the Open Source page!

Is Java still free and open source? I heard Oracle is charging for Java now!

Java is still free and open source. The only reason to pay Oracle for a Java license is to continue receiving commercial support from Oracle after January 2019 for the Oracle version of Java 8. If you use OpenJDK, you are fine. If you use an older version of Oracle Java 8 (such as the one currently shipping with Fiji), you are fine. See this article for details.

Why Do I Have To Download Java Jdk Mac Os

I would like to use the WatchService API as mentioned in this link:
http://download.oracle.com/javase/tutorial/essential/io/notification.html

After reading around, I found out that WatchService is part of the NIO class which is scheduled for JDK 7. So, it is in beta form. It’s fine.

http://jdk7.java.net/download.html has the JDK which I downloaded and extracted. I got a bunch of folders. I don’t know what to do with them.

Then, I read around some more and found that some nice group of people created JDK 7 as a binary so someone like me can install it easily. It is called Open JDK:
http://code.google.com/p/openjdk-osx-build/

So, I downloaded the .dmg file and install it. Then I open “Java Preference” and see that OpenJDK7 is available.

So, now I feel that I can start trying out WatchService API. From the tutorial in the first link, the author gave a .java file to test it out first and make sure that it is running. Here is the link to the file:
http://download.oracle.com/javase/tutorial/essential/io/examples/WatchDir.java

So, I boot up Eclipse (actually I use STS) and create a new Java project and choose JaveSE-1.7 in the “use an execution environment JRE:”. Under the src folder, I copy pasted the WatchDir.java file.

And I still see tons of squiggly red lines. All the “import.java.nio.*” are all red and I cannot run it as a Java app.

What do I need to do?

EDIT: I actually did not pursue using Java 7 but there are a lot of interest in it and it seems like people keep answering this question. What should I do to make it more relevant to people who search for it? Let me know by PMing me.

This is how I got 1.7 to work with Eclipse. I hope it helps.

1. I Downloaded the latest OpenJDK 1.7 universal (32/64 bits) JDK
   from Mac OS/X branch from http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html
2. copied the jdk to /Library/Java/JavaVirtualMachines/ next to the
   default 1.6.0 one
3. In Eclipse > Preferences > Java > Installed JREs you add a new one, of type MacOS X VM, and set the home as /Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home and
   name Java SE 7 (OpenJDK)
4. Click Finish
5. Set the added JRE as default

that should be it 🙂

You can download the Java Development Kit (JDK) for Java 8 for the supported versions of Mac OS X:

• Mountain Lion (10.8.3+)
• Mavericks (10.9)
• Yosemite (10.10)
• El Capitan (10.11)

Each version of JVM you install can be found here:

For more instructions and FAQ, see this Oracle Guide.

For every release of Java 7 since Update 4, a Mac version has been ready alongside the other platforms. Runs on Macs with 64-bit hardware on Lion (10.7.3+), Mountain Lion (10.8.3+), and Mavericks (10.9.x).

Oracle announced the official release of the JDK for Java SE 7 Update 4 on Mac OS X (Lion), as of 2012-04-26. No more need for the tricks discussed on this page.

Installation is simple per these instructions:

1. Download from the usual place on the Oracle web site.
2. Mount the DMG.
3. Run the installer.

This release has a few limitations, most notably the lack of support for Java Web Start and the Java Plugin for web browsers. That support is expected later this year.

After installing, read the JDK for Mac ReadMe. Most importantly, if you want Java 7 to be the default, drag it to the top of the list in the Java Preferences app found in your Utilities folder.

Mac OS X easily supports multiple JVMs simultaneously. Each is now found here:

Congratulations to the Apple & Oracle teams for their achievement. This geek gets a thrill seeing Mac OS X listed as a “Certified System Configuration“.

Tip: To start Eclipse on a Mac with only Java 7 installed, open the alias file named eclipse rather than the file named Eclipse.app.

Apple continues to supply an up-to-date implementation of Java 6 for all versions of Mac OS X up through Mountain Lion.

If you do something that requires Java, such as type “java -version” in Terminal.app, a dialog appears offering to install Java for you. If you accept, installation happens automatically similar to other “Software Updates” from Apple.

You will find Java installed in this location, different than Java 7 & 8:

Java 6 has reached end-of-life with Oracle as of 2013-02 (unless you have a commercial support agreement with Oracle). So you should be moving to Java 7 or 8.

In Terminal.app, type java -version to verify which version is the current default.

After installing a fresh version, you may want to visit the folder described above to delete old versions. Move the folder to the Trash, and provide your System password complete the move.

By the way, Apple provides a mailing list for developers’ technical issues related to Java on OS X.

An easy way to install Java 7 on a Mac is by using Homebrew, thanks to the Homebrew Cask plugin (which is now installed by default).

Run this command to install Java 7:

I know that some may want to smack me for re-opening old post, but if you feel so do it I just hope this may help someone else trying to set JDK 7 on Mac OS (using IntelliJ).

What I did to get this working on my machine is to:

• followed instructions on Oracle JDK7 Mac OS X Port for general installation
• in IntelliJ open/create new project so you can add new SDK (File > Project Structure)
• select Platform Settings > SDKs, press “+” (plus) sign to add new SDK
• select JSDK and navigate to /Library/Java/JavaVirtualMachines/JDK 1.7.0 Developer Preview.jdk/Contents/Home. Do not get it mistaken with /Users/YOUR_USERNAME/Library/Java/. This will link 4 JARs from “lib” directory (dt.jar, jconsole.jar, sa-jdi.jar and tools.jar)
• you will need also add JARs from /Library/Java/JavaVirtualMachines/JDK 1.7.0 Developer Preview.jdk/Contents/Home/jre/lib (charsets.jar, jce.jar, JObjC.jar, jsse.jar, management-agent.jar, resources.jar and rt.jar)

It’s possible that you still need to add the JDK into Eclipse (STS). Just because the JDK is on the system doesn’t mean Eclipse knows where to find it.

Go to
Preferences > Java > Installed JREs

If there is not an entry for the 1.7 JDK, add it. You’ll have to point Eclipse to where you installed your 1.7 JDK.

If Eclipse can’t find a JRE that is 1.7 compatible, I’m guessing that it just uses your default JRE, and that’s probably still pointing at Java 1.6, which would be causing your red squiggly lines.

after installing the 1.7jdk from oracle, i changed my bash scripts to add:

and then running java -version showed the right version.

Get cask

Install java7:

(I had difficulty finding the download link of java7 on oracle website, as they’re just “recommending” java8 )

How about Netbeans, here is an article how to set it up with NB7:

Maybe similar steps for Eclipse.

As of April 27th there is an offical Oracle release of Java SE 7u4. Download the disk image and run the installer – then see the Mac readme.

The instructions by peter_budo worked perfectly. I had to add the jars under /Library/Java/JavaVirtualMachines/JDK 1.7.0 Developer Preview.jdk/Contents/Home/jre/lib/ to my IntelliJ project libraries. Now it works like a charm. Note that I didn’t need my IDE itself to run under 1.7; rather, I only needed to be able to compile and run against 1.7. I’ll most likely continue to use Apple’s JRE for running the IDE since it’s probably more stable with respect to graphics routines (Swing, AWT). Like the OP, I was really keen on testing out the new NIO2 API. Looking good so far. Thanks, Peter.

What worked for me on Lion was installing the JDK7_u17 from Oracle, then editing ~/.bash_profile to include:
export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.7.0_13.jdk/Contents/Home

I updated to Yosemite and Android Studio wouldn’t clean my projects or Run them on virtual or real device because of the following error:

After some research and trouble shooting, I found that the JDK file that was being pointed to at “/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home” wasn’t there; all of “JavaVirtualMachines/1.6.0.jdk/Contents/Home” was missing from “/System/Library/Java”. So, I copied “JavaVirtualMachines/1.6.0.jdk/Contents/Home” over from “/Library/Java/” to “/System/Library/Java/” and cha ching! I was back in business.

Tags: osx