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OS X Installation OS X Installation. Installation Download ImageJ for Mac OS X from the page. The ZIP file you download (Image1.xx.zip) should automatically expand to a folder named 'ImageJ'. Copy this folder to the Applications folder, open it, and copy ImageJ.app to the dock. A 32-bit version of ImageJ ( ImageJ32.app), needed for running QuickTime plugins, is also available, but it is unabe to use more than 1800MB of memory.
With OS X 10.7 or later, the first time you run ImageJ, you may get get an 'ImageJ can't be opened because it is from an unidentified developer' message, which can usually be bypassed by right clicking on ImageJ.app and selecting 'Open' from the drop down menu. If that doesn't work, open the 'Security & Privacy' panel in System Preferences and change 'Allow apps downloaded from:' to 'Anywhere'. You can switch back to the original setting once ImageJ is running.
OS X 10.10 (Yosemite) and later do not include key files required for running commands like FileImportUsing QuickTime and FileSave AsQuickTime Movie that use QuickTime for Java. You can work around this problem by copying the files QTJava.zip and libQTJNative.jnilib, available at into /Library/Java/Extensions, where ' is your home directory. Yosemite hides the Library folder by default, so you will need to open your home folder and check 'Show Library Folder' in the ViewShow View Options dialog. Before copying the files, you will need to create the /Library/Java and /Library/Java/Extensions folders. MacOS 10.12 (Sierra) introduces a security feature called that can cause ImageJ to not work as expected.
Step through the installation steps, accepting the default settings. At one point it may ask to download a Java JDK program. Download and install that component as well. At the end, you should see an install successful message. At this point, you will start the Sfax for Mac installer file found here: Download Sfax for Mac. Download mac os. Java update mac. Related topics about Java Update for Mac OS X 10.5.
Path randomization is in effect if the 'ImageJ home' path shown in the ImageShow Info window starts with '/private' and plugins are not installed in the Plugins menu. You can disable path randomization by moving ImageJ.app out of the ImageJ folder and then copying it back. If the ImageJ folder is in /Applications you will need to hold down the alt key while dragging ImageJ.app out of the ImageJ folder. MacOS 10.13 (High Sierra) breaks Java 6, making it impossible to enter text into ImageJ dialog boxes.
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To work around this problem, use the version of ImageJ bundled with Java 8, available from the page. High Sierra also has the problem.
Memory Use the command to make more than default 3000MB of memory available to ImageJ. Note that setting the 'Maximum Memory' value to more than about 75% of real RAM may result in poor perfomance due to virtual memory 'thrashing'. The maximum amount of memory that can be allocated on 32-bit systems is about 1.8GB. Another way to make more memory available to ImageJ is by running from the command line and using the -Xmx option. The EditOptionsMemory command updates the VMOptions key in the Contents/Info.plist XML file in the ImageJ.app bundle. VMOptions -Xms256m -Xmx3000m You will get an error message if you do not have write permission for the ImageJ application. To check and/or change the permissions, open the ImageJ folder, select the ImageJ application, and use the Finder's FileGet Info command.
Upgrading Use the HelpUpdate ImageJ command to upgrade to the latest version of ImageJ. This command may fail with a 'Release Notes are not in the expected format' error if you are running a version of ImageJ earlier than 1.50i. You can work around this problem by using the plugin to upgrade. Drag and Drop The OS X version of ImageJ opens images, text files, ROIs and LUTs that are dropped on the ImageJ icon or on the 'ImageJ' window. Drag and drop TIFF files on the icon in the toolbar to open them as virtual stacks. Known Problems. The first time you run ImageJ you may get a message.
Plugins may not be installed when running macOS 10.12 (Sierra) due to. Text cannot be entered into dialog boxes on macOS 10.13 (High Sierra) when ImageJ is. Commands (e.g. FileImportVideo) and plugins that use QuickTime for Java fail with 64-bit versions of Java and with. Using command-v to paste text into the file name field of Save As dialog boxes does not work. This is a bug in the Java FileDialog class that can worked around by right-clicking in the name field and selecting 'Paste' from the drop down menu.
Adding JAR Files Some plugins require a Java code library contained in a JAR file (e.g., ). ImageJ's plugin class loader automatically loads code from such libraries as long as the JAR file is in the plugins folder or an immediate subfolder. The PluginsCompile and Run command also supports JAR file libraries located in the plugins folder or a subfolder.
Note that Compile and Run will not recognize the JAR file if the name does not end in '.jar' or if the name contains an underscore. Running from the Command Line To run ImageJ from the command line, open a Terminal window, cd to the ImageJ directory, then use the java command to run ImageJ. The easiest way to do this is to drag the ImageJ folder to the Terminal Window, type return, then type: java -jar -Xmx1024m ImageJ.app/Contents/Resources/Java/ij.jar or, with the version bundled with Java 8, type: java -jar -Xmx1024m ImageJ.app/Resources/Java/ij.jar The -Xmx1024m switch specifies that ImageJ will have available a maximum of 1024MB (1GB) of RAM.
Use a command like this to run ImageJ from any directory: java -Xmx1024m -jar /Applications/ImageJ/ImageJ.app/Contents/Resources/Java/ij.jar -ijpath /Applications/ImageJ ImageJ recognizes the following command line options: 'file-name' Opens a file Example 1: blobs.tif Example 2: /Users/wayne/images/blobs.tif Example 3: e81.tif -macro path arg Runs a macro or script (JavaScript, BeanShell or Python), passing an optional string argument, which the macro or script can be retrieve using the getArgument function. The macro or script is assumed to be in the ImageJ/macros folder if 'path' is not a full directory path. Example 1: -macro analyze.ijm Example 2: -macro script.js /Users/wayne/images/stack1 Example 2: -macro script.py '1.2 2.4 3.8' -batch path arg Runs a macro or script (JavaScript, BeanShell or Python) in batch (no GUI) mode, passing it an optional argument. ImageJ exits when the macro finishes.eval 'macro code' Evaluates macro code Example 1: -eval 'print('Hello, world');' Example 2: -eval 'return getVersion;' -run command Runs an ImageJ menu command Example: -run 'About ImageJ.' -ijpath path Specifies the path to the directory containing the plugins directory Example: -ijpath /Applications/ImageJ -port Specifies the port ImageJ uses to determine if another instance is running Example 1: -port1 (use default port address + 1) Example 2: -port2 (use default port address + 2) Example 3: -port0 (don't check for another instance) -debug Runs ImageJ in debug mode About the Icon The ImageJ icon for OS X is based on a photograph by of a Hartnack microscope, circa 1870's, at. A full size PNG version of the icon is available at.
Java is no longer installed with a OS X 10.11 El Capitan clean install, and you’ll find that after updating a Mac a prior version of JRE may no longer function. You may come across when trying to use some particular applications or web content, “This application requires the legacy Java SE 6 runtime which is unavailable for this version of OS X.” error message, which means if you want to run that app you’re going to need to use an older version of Java. If you do not need Java, you should not install Java.
Java is, and always has been, the source of many security holes. Here’s how you can install JRE (Java Runtime Environment). Step 1. Open Safari and go to the and download the JRE.tar.gz version. You should end up with a file named something similar to jre-8u65-macosx-x64.tar.gz. Go to your Downloads folder and extract the JRE download or use Terminal to extract files. / lib / server / libjvm. Dylib libserver.
Dylib You should be done now, so try and open the application. If it does not work, some applications require legacy Java 6 to be installed. You can have it installed without actually using it, however, it’s possible to trick the applications into thinking legacy Java 6 is installed, without actually doing so. (System Integrity Protection) in OS X El Capitan. Here is tutorial to. Step 2. Trick some applications into thinking that legacy Java 6 is installed by creating two folders with the following commands in Terminal.