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 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.
Windows
Run the installer (MM_Setup_x_y_zz.exe) and follow the prompts. The package includes a copy of ImageJ; it may be necessary to install or update Java on your computer. Besides the manufacturer’s low-level drivers for your camera and possibly other equipment, no other software is required to fully use Micro-Manager. Micro-Manager will be installed in C:\Program Files\Micro-Manager-x.y.
There are no particular hardware or software requirements. Micro-Manager works on Window 7 or 10 running as either 32-bit or 64-bit. However, some devices will only work using 32-bit drivers. Micro-Manager has also been reported to work with Windows Vista.
Currently, the Micro-Manager installer is not signed. This can cause issues with Windows not trusting the software. If you see the blue “Windows Protected your PC” dialog, click on “More Info”, which will unveil the “Run Anyway” button. If the “Windows Protected your PC” dialog is red, you have multiple options. You can go to Windows Settings, Update & Security, Windows Security, App & Browser control, Reputation based Protection Settings, switch off “Check apps and files”. Or, you can right click on the installer and select “Unblock”.
If the application looks too small, use the Windows File Explorer and locate the installation directory (such as C:\Program Files\Micro-Manager). Right click on ImageJ.exe, select Properties, select the Compatibility tab, ensure that “Use this setting to fix scaling problems…” is checked and click OK or Apply (you may want to do this “for all users”).
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 ImageJ.app 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.
On MacOS Catalina 10.15.7, and later, the gatekeeper then complains that nothing is signed by a verified developer. The solution to that involves a very large amount of clicking (you have to click several buttons per device adapter to tell gatekeeper that you really do want to run them…)
There is a better solution: open a terminal and run
sudo xattr -r -d com.apple.quarantine <Path to Micromanager Install>
for instance:
sudo xattr -r -d com.apple.quarantine /Applications/Micro-Manager-2.0.0
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.
Linux
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.