Imagej Download Windows

[Marguerite Gilbeau]

Mac OS XDownloadImageJ bundled with Java 8(may need to work around Path Randomization). Instructions. With M1 (ARM) Macs, downloadImageJ bundled with Zulu OpenJDK 13.0.6.LinuxDownload ImageJ bundled with Java 8.Instructions.WindowsDownloadImageJ bundled with 64-bit Java 8.Instructions.DocumentationTiago Ferreira's comprehensive ImageJ User Guideis available as an 8MB PDF document and as a ZIP archive.The onlineJavaDoc API documentation is also available as aZIP archive.Source CodeThe ImageJ Java source consists of 160,000 linesof code in 380 files (LineCounter macro).It is availableonline andas zip archives.Example Images31 downloadable sample images and stacks are available in ImageJ's File>Open Samples submenu. These images, and more, are also available as a 8.2MB zip archive.You can also browse the ImageJ download directory atimagej.net/ij/download/.Newer ImageJ distributions are available at to the Release Notesfor a list of new features and bug fixes. top home docs download plugins resources list links

If the "ImageJ" window is too small, set "GUI scale" inthe Edit>Options>Appearance dialog to a value greater then 1.0.Use the Help>Update Image command to upgradeto newer versions of ImageJ.MemoryUse the Edit>Options>Memorycommand to make more than the default 640MB 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 Edit>Options>Memory command modifies the third line in the ImageJ.cfgfile in the ImageJ folder, which must be writable.This is what ImageJ.cfg looks like with "Maximum Memory" set to 1500MB: . jre\bin\javaw.exe -Xmx1500m -cp ij.jar ij.ImageJYou may get an error message that looks something like this: Unable to update the file "ImageJ.cfg C:\Program Files\ImageJ\ImageJ.cfg (Access denied)This error is the result of not have write access to the folder containing ImageJ.You need to either run ImageJ as an administrator, or to install it in a folderthat you do have write access to, for example the Documents folder.TroubleshootingHere are some common problems encountered when running ImageJ on Windows, and their solutions:

• ImageJ does not start. Delete the ImageJ.cfg file in the ImageJ folder.
• The "ImageJ" window is tiny on my high resolution screen. Upgrade to Windows 8.1 or later, open theImageJ.exe>Properties>Compatibility panel and uncheck"Disable display scaling on high DPI settings".
• Cannot increase memory in Edit>Options>Memory & Threadsor ImageJ unexpectedly runs out of memory. Install ImageJ in a directory that you have write access to,such as "Documents" or "Desktop".
• ImageJ displays blank windows or windows filled with garbage. Update video card driver or try running the nVidia Fix plugin
• Multiple copies of ImageJ are started when I open images by double clickingon them or by dragging and dropping them on the ImageJ icon. Enable "Run single instance listener" in Edit>Options>Misc.
• I installed a 64-bit version of Java but ImageJ is using the 32-bit version. Edit the second line of ImageJ.cfg to point to the 64-bit version ofJava. For example, change "C:\Program Files (x86)\Java\jre7\bin" to"C:\Program Files\Java\jre7\bin".
• I installed the Windows 10 Creators Update andnow ImageJ freezes when I try to open an image. Enable "Use JFileChooser to open/save" in Edit>Options>Input/Output.Drag and DropThe Windows version of ImageJ opens images, folders of images, text files, ROIs and LUTs dropped on the "ImageJ" window or on the the ImageJ application icon.Upgrading to a Newer Version of JavaThis is what you need to do to upgrade to a newer version of Java:
  • Download and install the latest JDK from www.oracle.com/technetwork/java/javase/downloads/
  • Go to the ImageJ folder and delete or rename the jre folder
  • Delete the ImageJ.cfg file
  • Restart ImageJ and the launcher (ImageJ.exe) will generate a new ImageJ.cfg that uses the Java you just installed.
  Contents of ImageJ Folderij.jarThis JAR (Java Archive) file is the platform-independent core of ImageJ. It is theonly file changed when you upgrade using the Help>Update ImageJcommand.ImageJ.exeThis is the ImageJ launcher.jre (optional)This folder contains the Java runtime.macrosThis folder contains example macros. The StartupMacros.txt file in this folder contains macros and macro tools that are automatically installedwhen ImageJ launches. To run a macro, drag and drop it on the ImageJwindow and run it by pressing ctrl-r (Macros>Run Macro).pluginsThis folder contains a small sample of the hundreds of pluginsavailable for ImageJ. Plugins, macros and scripts in this folder, and immediatesub-folders, are installed in the Plugins menu when ImageJ launches.lutsThis folder contains LUTs (LookUp Tables) that are installed at startup in theImage>Lookup Tables menu. Use the Image>Color>Display LUTscommand to view all the LUTs in this menu.Command Line OptionsTo run ImageJ from the command line, open a Command window, change to the ImageJ directory, and enter a command something like this: jre\bin\java -jar -Xmx1024m ij.jarThe -Xmx1024m switch specifies that ImageJ will have available a maximum of 1024MB (1GB) of RAM.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 top home news docs download plugins resources list links

Are you obtaining ImageJ from the Downloads page of the ImageJ wiki? It works on my Windows 10 system, as long as you place it somewhere you have write permission, such as C:\Users\\Fiji.app, and not in C:\Program Files.

Hi, Can I revive this topic?
After reading through the above. Ive tried both the vanilla ImageJ2 and the most recent Fiji versions on Windows 10, (Microsoft Surface Pro). I cant get either to start up. For example, the error Im getting is

I have not observed this problem with spaces in the user name. @awm27 What is your exact user name here? Is it really XYZ? Or something else? Do you have any non-ASCII characters in the name? Does it work as @BishopWolf suggests to move the folder somewhere else before running ImageJ-win64.exe?

tested! copy Fiji.app to D:\_My fiji@\Fiji.app and it opens fine, no problem at all. Moreover, copy to C:\_My fiji@\Fiji.app and it opens fine too. I even replicate his folder and it opens fine also, Windows 8.1 x64 here. Seems this old linux bug was not part of Fiji and since I always have my fiji in D:\Fiji.app I never worried about it.

I am having a similar issue with installing Fiji Imagej. I started by trying to download the NIH website version on my microsoft surface book with windows 10, but when I would go to run the application, nothing would happen that I could see. Task manager would show that ImageJ was running but I had no way to find the toolbar. So I found this thread, uninstalled that and downloaded the fiji version that was recommended. I followed the suggestions on where to place the file. This time the Fiji logo at least appeared, but again, I cannot find the toolbar.

It is possible ImageJ is appearing off the screen. Did you have a second monitor plugged in, and then later unplugged it? You could try pressing Alt+space, M, enter, and then move the mouse to bring the window back to your visible monitor. You could also try clearing the preferences by deleting the IJ_Prefs.txt file from the appropriate location (see the docs), which will force ImageJ to recompute the preferred location of its main window.

The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants, including ImageJ2, Fiji, and others.

If you are installing ImageJ2 on Windows, we strongly recommend that you storeyour ImageJ2.app directory somewhere in your user space(e.g., C:\Users\[your name]\ImageJ2.app) rather than in C:\Program Files orother system-wide directory. If you move ImageJ2.app to such a directory, modernversions of Windows will deny ImageJ2 write permission to its own directorystructure, preventing it from being able to update. See alsoimagej/imagej#72.

Running an original ImageJ style macro is as simple as providing the macro code in a string, and the arguments in a dictionary to ij.py.run_macro. Modify the following cell to print your name, age, and city.

When you call run_script, the entire script executes on the Java side in one shot, whereas the equivalent Python code would perform many calls across the Python/Java boundary, each of which takes some extra time and might fail due to bugs in PyImageJ/scyjava/JPype/etc. Therefore, depending on the situation, run_script might improve performance and/or correctness.

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