ImageJ for Mac OS X ImageJ 1.41is a free Java image processing program. The program runs as an online applet or as a downloadable application, on any Java enabled computer (with Java 1.4 or later virtual machine). ImageJ can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images.
Critical: if you update and Fiji does not work anymore, you need to follow these instructions.
- ImageJ for Mac OS X freeware download - Best Freeware Download - Freeware downloads - best freeware - Best Freeware Download.
- Download Platform Independent To install ImageJ on a computer with Java pre-installed, or to upgrade to the latest full distribution (including macros, plugins and LUTs), download the ZIP archive (6MB) and extract the ImageJ directory. Use the HelpUpdate ImageJ command to upgrade to newer versions.
- Download ImageJ for Mac to perform scientific pixel-by-pixel image processing and analysis. ImageJ has had 2 updates within the past 6 months. OS X El Capitan OS X Yosemite OS X Mavericks OS X.
- 3Limited PowerPC (G4/G5) Mac support
Installing Fiji
- Download the .dmg package from the Downloads page, and then double-click it to open it.
- Create a folder under /Applications/, such as /Applications/Fiji
- Drag the 3 items (Fiji.app, and the plugins and macros symlinks) into the /Applications/Fiji folder.
Fiji is ready to run!
Running Fiji in 32-bit mode
Fiji on Intel Macs runs on Java 1.6 in 64-bit mode. If you need to run it in 32-bit mode, you can do so as follows:
- Launch Fiji normally, and choose Edit › Options › Memory & Threads.
- Reduce your Maximum Memory setting to ~1800 MB or less.
- Quit Fiji.
- ^ Ctrl+click the Fiji dock icon and choose Options › Show in Finder.
- ^ Ctrl+click on the Fiji application icon that pops up, and choose Show Info (or press ⌘ Cmd+I).
- Check the 'Open in 32-bit mode' box in the Fiji info window.
- Press the red X on the Fiji info window to close it.
- Launch Fiji again, and the status bar should report '[32-bit]' in brackets.
Alternately, you can execute the following code from the Terminal:
Either way, you will need to make sure your maximum memory limit is set below ~1800 MB. If your maximum memory is set higher than the 32-bit limit, Fiji will not be able to start up successfully in 32-bit mode.
Limited PowerPC (G4/G5) Mac support
We offer a special intermediate release of Fiji specific to PowerPC Macs (G4/G5).
Note: There is no Java 1.6 for PowerPC from Apple, meaning that Java comes at a considerable performance penalty on this platform. In addition, we will not be able to support Java versions prior to Java 1.6 at some stage, since that version offers a few features we want to rely on, such as a versatile scripting framework.
Advanced
You can also install a third party Java 6, part of the OpenJDK project. You will need a working X11 server, that you can find on your OS X disk, and MacPorts.
Execute sudo port install openjdk6 on your Terminal. You can also install the SoyLatte Binaries, as an alternate choice.Then you can proceed with the generic Fiji Installation
Check more info at landonf.bikemonkey.org/static/soylatte/
Accessing the plugins and macros folders
To access the plugins or macros folders, set the Finder window to either icons or lists mode, not in column mode, and double-click them.
Alternatively, right-click (or ^ Ctrl+click) the Fiji.app and select 'Show package contents', to open the folder where the actual plugins and macros folders are.
Adding new plugins and macros
For plugins, please follow the instructions about Installing 3rd party plugins. Otherwise, access the plugins folder as explained above and just drag and drop any plugin into the plugins folder, like you would do for ImageJ. Same for macros.
Installing OpenJDK for MacOSX
Imagej Download Windows
Oracle now supports MacOSX JavaSE 7 officially.
It is based on an Apple-backed effort to get a proper MacOSX backend into the BSD port of OpenJDK. So far, only Snow Leopard and later are supported, and preliminary builds can be found here.
If you are experiencing problems, say, with AWT-AppKit related crashes, and if you do not mind working with an X11-based graphical user display, you might want to try OpenJDK.
As of mid-April 2011, OpenJDK for MacOSX has basic working support for Aqua, which you have to activate explicitly by passing the Java option -Dswing.defaultlaf=com.apple.laf.AquaLookAndFeel.
Since the development of OpenJDK for MacOSX is driven exclusively by Apple employees, the minimal MacOSX version required to run OpenJDK/Aqua is 10.6. If you require Fiji to run on earlier versions of MacOSX, you will have to go back to SoyLatte, where you will also find an X11-only OpenJDK version that runs on MacOSX 10.5/PowerPC (MacOSX 10.6+ does not support PowerPC). In the alternative, you can put in a considerable effort to 'backport' OpenJDK :-).
Running Fiji in the command line
Often it is necessary to run Fiji in the command line, e.g. to pass some command-line options. To do so, start a Terminal (in the Finder, Go>Utilities), and switch to the correct directory using the cd command. Note that the application itself is actually a directory called Fiji.app. For example, if you installed Fiji into /Applications as recommended, do this:
If you unpacked Fiji onto your desktop, do this:
Once you switched to the correct directory, start the Fiji launcher:
Note for Windows users: A backslash is not the same as a slash. So: ContentsMacOSImageJ-macosx will not work.
Imagej Plugin Download
Now you can pass, say, Java Options:
Note: to distinguish between options intended for Java and options intended for ImageJ, you need to separate the former from the latter with a double-dash: --. Since the default is to accept ImageJ options, you have to pass a trailing double-dash if you want to pass only Java options.
MacOSX keyboard shortcuts
It is often helpful to use keyboard shortcuts when using Fiji. There are also operating system specific shortcuts which can be quite helpful. For example, pressing ⌘ Command+Tab ↹ and releasing first only the Tab ↹ key will allow you to cycle through the running applications, while ⌘ Command+` will do the same for the windows opened by the current application. Dave Polaschek has a comprehensive list.
| About | |
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| ImageJ | |
| Usage | |
| Contributors | |
| Governance | |
| Funding | |
| Citing | |
| Contributing | |
| Wish list | |
ImageJ is an open source Java image processing program inspired by NIH Image. It runs on any computer with a Java 1.8 or later virtual machine. Downloadable distributions are available for Windows, Mac OS X and Linux. ImageJ has a strong, established user base, with thousands of plugins and macros for performing a wide variety of tasks.
Flavors
There are a few different flavors of ImageJ with very similar names, and some confusion is inevitable. Below is a table which should help to clarify the purpose of each. For the historical context of these projects, see History below.
| Name | Author/Maintainer(s) | Description | Initiated | Status | |
| Fiji | Fiji contributors | Fiji is Just ImageJ, with extras. It is a distribution of ImageJ with many plugins useful for scientific image analysis in fields such as life sciences. It is actively maintained, with updates released often. We recommend Fiji as the preferred version of ImageJ. | Dec. 2007 | Active | |
| ImageJ2 ImageJDev | ImageJ developers | A new version of ImageJ targeting scientific multidimensional image data. It is a complete rewrite of ImageJ, but includes ImageJ1 with a compatibility layer, so that old-style plugins and macros can run the same as always. ImageJ2 provides several significant new features, such as an automatic updater, and improved scripting capabilities. | Dec. 2009 | Active | |
| ImageJ1 | Wayne Rasband | A stable version of ImageJ which has been in development since 1997. It has a strong, established user base, with thousands of plugins and macros for performing a wide variety of tasks. | 1997 | Active | |
| ImageJA | ImageJ developers | ImageJA is a project that provides a clean Git history of ImageJ1, with a proper 'pom.xml' file so that it can be used with Maven without hassles. It is what ImageJ2's legacy support uses at its core. | Jul. 2005 | Active | |
| ImageJFX | Cyril Mongis | ImageJFX is a new user interface for ImageJ, built using JavaFX. | 2015 | Active | |
| ImageSXM | Steve Barrett | Image SXM is a version of NIH Image that has been extended to handle the loading, display and analysis of scanning microscope images. | May 1993 | Active | |
Error creating thumbnail: Unable to save thumbnail to destination | AstroImageJ | John Kielkopf | AstroImageJ is ImageJ with astronomy plugins and macros installed. | Unknown | Active |
| ImageJ2x | Rawak Software | ImageJ2x is a fork of ImageJ1, modified to use a Swing interface. | Unknown | Last update: May 2015 | |
| Closed-source variants | |||||
|---|---|---|---|---|---|
| SalsaJ | EU-HOU | SalsaJ is a closed-source fork of ImageJ1 intended for use with professional astronomy images. It was designed to be used in classrooms, and has been localized into over 30 different languages. | Unknown | Last update: Oct. 2012 | |
| Obsolete variants | |||||
| MBF ImageJ | Tony Collins | The MBF 'ImageJ for Microscopy' bundle (formerly WCIF ImageJ) is a collection of plugins and macros, collated and organized by the MacBiophotonics facility. It went hand in hand with a comprehensive manual describing how to use the bundle with light microscopy image data. It was a great resource by microscopists, for microscopists. Unfortunately, the manual went offline in late 2012. In response, the software team at LOCI created the Cookbook user guide and update site, which includes most of the same plugins. | 2005 | Defunct (Last update: | |
| ImageJX | Grant Harris | ImageJX was created as a means to discuss and explore improvements to ImageJ. There was an ImageJX mailing list as well as an ImageJX software prototype. The ImageJX software prototype was a proof of concept—an attempt to reorganize ImageJ's internals to make it more flexible. The prototype demonstrated this flexibility by recasting the program in Swing. The ImageJX project formed the basis of an application to NIH for funding, which is what launched the ImageJ2 project (see above). | Mar. 2009 | Superceded by ImageJ2 | |
| NIH Image | Wayne Rasband | NIH Image is a public domain image processing and analysis program for the Macintosh. It is the direct predecessor of ImageJ, and is no longer under active development (though see ImageSXM below). | 1993 or earlier | Superceded by ImageJ | |
History
The first imaging program that Wayne Rasband developed, starting in the late 70s, was called simply 'Image'. It was written in Pascal, ran on PDP-11 minicomputers and ran in only 64KB of memory! Rasband started work on the second, NIH Image, in 1987 when the Mac II became available. Rasband was a Mac enthusiast, and the Mac II had card slots just like the PDP-11. Rasband started work on ImageJ in 1997, when Java was becoming popular. Rasband was intrigued by the idea of creating a version of NIH Image that would 'run anywhere', including as an applet in Web browsers.
Imagej Software Download
Timeline
Here is a timeline of software development related to ImageJ:
Publications
- Schneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), 'NIH Image to ImageJ: 25 years of image analysis', Nature methods9(7): 671-675, PMID 22930834, <http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2089.html>.
- Schindelin, J.; Rueden, C. T. & Hiner, M. C. et al. (2015), 'The ImageJ ecosystem: An open platform for biomedical image analysis', Molecular Reproduction and Development, PMID 26153368, <http://onlinelibrary.wiley.com/doi/10.1002/mrd.22489/full>.
See also Citing.