Imaging cells has become an essential technology in many laboratories working in the life sciences. The components needed for such image acquisition consist of a microscope, cameras, light sources, mirrors, filters mounted in motorized filter wheels, x-y-z stages, and shutters. In practice, many complicated sequences of motorized operations are needed to achieve the imaging strategy desired by the researcher (e.g. acquiring images from multiple wavelengths). Thus, computer control of image acquisition is an integral part of contemporary microscopy.
From the user’s standpoint, the whole setup (a microscope equipped with camera, stage, filter wheels,
etc.) ideally should appear as an integrated, coherent system – an “appliance.” This appliance should allow for effective and comfortable interactive work, as well as unattended, completely automated operation.
Available commercial packages more or less provide the needed functionality for controlling automated microscopes, but, because they are proprietary and closed, they are difficult to extend and customize. New devices cannot be added to the system unless the software vendor chooses to provide appropriate drivers. Sometimes the cost of configuring the system with all necessary software and drivers can be quite high.
In contrast to virtually all of the available commercial solutions, Micro-Manager supports multiple platforms (Windows, Mac and Linux) and provides an open plugin interface for adding new devices. In addition, Micro-Manager is compatible with the widely used image processing package ImageJ, which is also available in the public domain. Combined with ImageJ, Micro-Manager provides a full-featured microscope management and image processing package, comparable in capabilities to commercial solutions. It is distributed free of charge and under an Open Source license. Its code base and functionality can be customized, extended and re-used with practically no restrictions.
After you install Micro-Manager according to the instructions for your platform (below), you can test-drive the software in demo-mode. The application will start in demo-mode by default after initial installation. To use Micro-Manager with your microscope, you will need to create a configuration file for the hardware components that are part of your setup.
The configuration process is described in the Configuration Guide. You will need to create a configuration file specific to your system.
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”.
Double click on the file Micro-Manager1.x.yy.dmg. 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 (to run a 32-bit version of Micro-Manager) or by clicking the ImageJ64 icon (to run the 64-bit version).
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 command (or ctrl, or option) 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>
sudo xattr -r -d com.apple.quarantine /Applications/Micro-Manager-2.0.0-gamma1-20210309
Micro-Manager is packaged as an ImageJ plug-in and contains a copy of the entire ImageJ application, together with the Java run-time environment. Starting Micro-Manager will automatically start ImageJ as well. If you already use ImageJ and have it insta