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This guide is intended to help you quickly start imaging with μManager on a basic wide-field microscope/camera system. µManager can also be used to control devices on time-lapse microscope systems, but that is too advanced to be dealt with here. If you're interested in finding out how to configure hardware in µManager there is a comprehensive user guide on the µManager website.

Make sure the camera is on before opening µManager. If you're using Windows then double-click the µManager icon on the desktop. If you're using a Mac then you can click its icon in the dock. Note that the icon may say 'ImageJ' when you hover the mouse over it - that's normal.

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Micro-Manager Windows and Mac iconsImage Modified

µManager icons - Windows (left) and Mac (right)

µManager configuration

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Select the correct configuration from the drop-down list that appears with the splash screen. The image below shows configuration for the QIClick on the Axioplan microscope. If the configuration you want isn't listed you can browse for it by clicking the button to the right of the list. If you want to process data without turning the camera on you can select '(none)' from the list.

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 Micro-Manager configurationImage Modified

µManager user interface

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The image on the right shows a typical µManager GUI. The details of the Groups and Presets may vary from system to system. Select the right Magnification Preset to match the objective lens and optovar (if applicable). Make sure the camera depth is set to its maximum (usually 12-bit). Click Live to get a live image. Click the Zoom tools to make the live image bigger or smaller. Set the exposure by typing a value in the field and change the binning if necessary. There may be a gain control. Click the Auto button next to the live image contrast histogram to auto-contrast the image once, or you can tick Autostretch to have auto contrast on constantly (see below).

Auto contrast tools

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Micro-Manager GUIImage Modified

Image acquisition using the Album button

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The best way to acquire images is click the Album button at the bottom of the live image window (see below). This creates a new window containing the image you just captured. As you keep clicking the button the images are added to the window and can be saved either as a stack or individual TIFF files by clicking the disc icon. It's best if you save the image as a stack if possible because this will open correctly when you use the Bioformats Importer in Fiji or ImageJ. Otherwise you can make a copy of the data using the ImageJ Duplicate... command in the Image menu, but you will need to fill in the number of slices in the Range field.

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Live image album and save buttonsImage Modified

The bottom of the Live window with Save icon (left) and Album (right)