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Micro-Manager Installation Notes

After you install Micro-Manager using the instructions for your platform, you can test-drive the software in demo-mode. The application will start in demo-mode by default after installation. To use Micro-Manager with an actual microscope you will need to configure the software for the specific hardware components that are part of your setup.

The configuration process includes editing configuration files and is described in the [documentation.php?object=Configguide Configuration Guide]. Installation includes a number of sample hardware configuration files (with extension *.cfg) provided only as an example or starting point - they need to be edited in order to use the system with any particular hardware setup.


Run the installer (MMSetup_xxxx.exe) and follow the prompts. The package includes a copy of ImageJ and Java. You might need to install drivers for your cameras and possibly other equipment (see our Device Support page).

Micro-Manager is intended for Windows XP and later. Some versions may work on Windows 2000 (by installing some additional components), but this is untested and unsupported.

There are no particular hardware requirements. However, for practical use we recommend a 1.7-GHz or better processor and at least 512 MB of RAM. Depending on your camera (image size) and imaging speed, you may want to have a lot more RAM.

Mac OS X

Double click the file Micro-Manager1.x.x that you just downloaded (see Download Micro-Manager Latest Release). This will open a drive called 'Micro-Manager'. The drive is on the desktop and in every Finder Window. Open the drive (by double-clicking). In the drive there is a folder called Micro-Manager1.x. You can install the application by dragging this folder to your Applications folder, or you can launch the application by opening the folder and double clicking the 'ImageJ' icon. If you want to run the 64-bit version of Micro-Manager, click the "ImageJ64" icon.

Mac OS X security policies mandate a couple of extra steps (which may be different in different versions of the OS). Go to "System Preferences" > "Security&Privacy" Click the lock in the bottom left corner, provide an administrator password, then start up the ImageJ app. When you go to "Plugins" in the menu, and see the item "Why are plugins missing?", you will need to quit ImageJ and move the to the desktop, then move it back. On some Macs you will need to press the option (or ctrl) key while dragging the app to actually move it rather them make a shortcut (don't ask me why, but Macs have become very confusing machines). If Micro-Manager still does not start, check the Java version by clicking in the lower part of the ImageJ window. If you see that the Java version is 1.6, you need to install Java 8. Currently, you can get this from multiple sources, I like adoptopenjdk. Download and install the latest version. If ImageJ still picks Java 6, try copying the "jre" directory of the adoptopenjdk installation into the Micro-Manager directory.

By default, after the first installation Micro-Manager starts with the Demo configuration which loads software simulators for a number of commonly used devices. This configuration can be used to explore Micro-Manager features, train novice users and as a reference point for troubleshooting.


Micro-manager should work with most standard Linux distributions (e.g., Ubuntu, Fedora, Gentoo). However, no pre-compiled version is provided, and you need to compile and install it from source. See:

If you already use ImageJ

Micro-Manager is packaged as an ImageJ plug-in and contains a copy of the entire ImageJ application, together with the Java run-time engine. Starting Micro-Manager will automatically start ImageJ as well. If you already use ImageJ and have it installed on your machine beforehand, the original installation will not be affected. Micro-Manager installs and uses its own copy of ImageJ. However, if you have any existing ImageJ macros or plugins that you want to use with Micro-Manager, you will have to copy them manually to the appropriate sub-folders within the root Micro-Manager folder.

Migrating your favorite ImageJ plugins to Micro-Manager installation should not cause any problems.

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