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Unformatted text preview: Micro-Manager Manual Hernan G. Garcia March 30, 2009 Introduction: Why Micro-Manager? Micro-Manager (MM) is a microscope control software developed in Ron Vales Lab at UCSF with support form NIH. The idea was to provide a free, open-source platform based on Java using ImageJ (which is also funded by NIH). Basically, MM tries to imitate the function of packages such as Meta- Morph, ImagePro and SlideBook, but for free whereas these other packages go for up to $10,000. In Bi1X we will be using mostly the GUI user interface. However, MM has a good scripting language. Its libraries for microscope control can also be accessed from Matlab, giving the chance to integrate data acquisition and data analysis. Because its a program in constant development it will always have some bugs. Please report any of them to the TAs so we can pass that information along to the programmers and, also, be patient! The next few paragraphs give guidelines to be followed every time you sit in front of the microscope. Some safety words Three of our scopes (Kratos, Nemesis and Wheels) use external filter wheels. This means that when using fluorescence if you look through the eyepiece you might get some of the UV excitation light. DO NOT LOOK THROUGH THE EYEPIECE WHEN USING FLUORESCENCE . This is not a concern in the Zeiss. After turning on the fluorescence lamp it should be kept on for at least 30 minutes. When turned off it should be kept off for at least 30 minutes. Changes to the bulb before its equilibrated can break it. 1 Turning everything on Theres no particular order you should turn things on. However, make sure to turn on the fluorescence only if you need it and to turn everything off once youre done with your experiment....
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- Fall '09