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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 configuration guide on the µManager website.

Make sure the camera is switched 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 click the 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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Select the correct configuration from the drop-down list that appears on top of the splash screen. The image below shows a 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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The image on the right shows a typical µManager GUI. The details of the Groups and Presets may vary from system to system. Select a magnification preset to match the objective lens and optovar (if applicable). Make sure the camera depth is set to the best quality (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 also be a gain control. Click the Auto button next to the live image histogram to automatically adjust the contrast of the image once. Tick the Autostretch box to leave auto contrast on constantly.

","reason":"A column macro in a rich body macro can't be created or edited in the new editor.","nestedContent":{"type":"doc","content":[{"type":"bodiedExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"column","parameters":{"macroParams":{},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Column"}}},"content":[{"type":"paragraph","content":[{"text":"The image on the right shows a typical µManager GUI. The details of the Groups and Presets may vary from system to system. Select a magnification preset to match the objective lens and optovar (if applicable). Make sure the camera depth is set to the best quality (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 also be a gain control. Click the Auto button next to the live image histogram to automatically adjust the contrast of the image once. Tick the Autostretch box to leave auto contrast on constantly.","type":"text"}]}]}],"version":1}}}},{"type":"extension","attrs":{"extensionType":"com.atlassian.confluence.migration","extensionKey":"legacy-content","text":"","parameters":{"cxhtml":"50%

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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 creates an OME TIFF file (from the Open Microscopy Environment) that will open correctly when you use the Bioformats Importer in Fiji or ImageJ. Otherwise you can make a copy of the data in ImageJ using the Duplicate... command in the Image menu, but you will need to fill in the number of slices in the Range field.

","reason":"A column macro in a rich body macro can't be created or edited in the new editor.","nestedContent":{"type":"doc","content":[{"type":"bodiedExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"column","parameters":{"macroParams":{},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Column"}}},"content":[{"type":"paragraph","content":[{"text":"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 creates an OME TIFF file (from the ","type":"text"},{"text":"Open Microscopy Environment","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.openmicroscopy.org/site"}}]},{"text":") that will open correctly when you use the Bioformats Importer in Fiji or ImageJ. Otherwise you can make a copy of the data in ImageJ using the Duplicate... command in the Image menu, but you will need to fill in the number of slices in the Range field.","type":"text"}]}]}],"version":1}}}},{"type":"extension","attrs":{"extensionType":"com.atlassian.confluence.migration","extensionKey":"legacy-content","text":"","parameters":{"cxhtml":"50%

Micro-Manager Quick Start

A quick guide to capturing images with μManager

µManager configuration

µManager user interface

Image acquisition using the Album button