1. Microscope Control Configuration This section of the QED manual will describe how to configure you Configure and Control your automated microscope. Mac or Windows installer depending on your system. The first 4 pages are a quick review of the Microscope Control and Configuration Tools. The next pages will go into details of define individual devices. ConfigureControl Microscope Control

2. Setup window 1) Select the Setup window to define your camera, microscope and any additional hardware configuration. 3) Select The Full Setup options to show to multiple microscope components and custom configuration of these components. In this tutorial we will not define any microscope configurations. 2) Select your camera from this dropdown menu. The program will perform system check and alert you if there are any problems with the camera. The calibration settings can be used to match the size of the pixels and the distance between pixels to actual metric values. Microscope Control The setup tool allows you to define your system configuration, including the camera and microscope hardware. You also calibrate each magnification for correct pixel to real distance conversion. In this section you can define your camera. You can also explore the Microscope Configuration but for the tutorial will use the simulated controls.

3. Full Microscope Configuration window This section describes the general Configuration of an automated microscope. The default devices can be added to the configuration by selecting the Manufacturer and the Type. Multiple communication options are available. Each device can be configured individually or the software can automatically configure it. Controller Types/ Manufacturers Default Microscope Devices Communication Serial/USB/Board Device Settings Auto Configuration Microscope Control 1) Click the “Clear All Settings” button to remove all simulated controls.

4. Configuring Automated Microscopes QED supports the automated configuration of automated microscopes from various vendors. Once you select your microscope the software will communicate with the microscope controller and find out which devices are available. The software will then ask you if you want to use each device. You will also be able to select a scanning stage. 1) In the Automated Microscope window select your microscope. 2) Select the connection type, usually a COM port. 3) Click the Auto Config button to start the configuration. The software will guide you through the configuration. 4) In the Scanning Stage item select your stage. 5) Select the connection type, usually a COM port. 6) Click settings to home the stage.

5. Configuring Individual Devices Once you have defined your devices through the Auto Config option or manually, you can set the parameters for each device individually. This will allow you to set additional information such as shutter speed, number of objective positions, filter information, etc. The resulting Configuration matrix should look similar to the one below for automated microscopes with a scanning stage. Note that the communication connections will vary based on the device. 1) Click on the individual Settings buttons for each device to set addition parameters. 2) Additional items like a third and fourth shutter can be added through a configuration file. Sample files are located in the QED Help folder.

6. 1) Start QED by clicking the Microscope icon in the Main Toolbar. This will open up the Microscope Control Dialog. Microscope Control Window 2) Individual devices can be controlled by clicking on the actual representation. Click on the Bright field shutter Icon to close and open the shutter. 1) Change the default microscope configurations by selecting a different stored configuration. If you have a Number Keypad on your keyboard, you can also hit a number to change the microscope configuration. The QED Microscope Control Module provides interactive and automated control for a variety of microscope systems. Software controls include multiple shutters, filter wheels, filter cube changers, scanning stage, focus control, objective selection, etc. 3) Click on the Fluorescence shutter to open and close it. Microscope Control

7. Configuring Devices in the Microscope Control Window 1) Click on the Shutter while holding down the “Ctrl” key. The Shutter configuration dialog allows you to define the time it takes to open and close the shutter. Within the Microscope Configuration window you can change the parameters of the individual devices. This is done when you need to change the position of a filter from the default configuration or if you change an objective or ND filter. Microscope Control 2) Click on the Objective while holding down the “Ctrl” key. The Objective configuration dialog allows you to define parameters related to your objective need for deconvolution, auto focusing etc.

8. Define and Store Microscope Configurations. Once you have set up your microscope and devices you can create Microscope Configurations. Microscope configurations are “snapshots” of states of the microscope. For example, a state can have the DAPI filter in the light path, the Fluorescence shutter open, the camera on port 2 in use, and the objective turret set to the 40X objective. 1) Use the Microscope Control Tool to change the individual devices in a specific microscope configuration. This can include settings for the following devices: Filter wheel, Filter cube, Objective turret, Camera port changer, etc. 2) Click the Define button to store this new configuration or to update an existing one. 3) Create a new name or leave the name as is to update an existing configuration. 4) Check the new entry button to create a new configuration. 5) Check default to use the new configuration at startup. 6) Define the Acquisition type when taking this Image. 7) Once you create a new configuration it will be assigned to a number key and it can be used throughout the software.

9. Using the Stored Configurations for acquisition. 1) Click on the MIC buttons to see the associated Microscope configuration for each Image Channel. Every Microscope Configuration can be assigned to an Imaging Mode. An Imaging Mode is an Acquisition with pre-defined parameters like: exposure time, binning, gain etc. The Imaging Modes Tool uses the first three Microscope Configurations for the first three colors. You can change the order or you can select your new Microscope Configuration. 1) Click the Acquire all button to acquire the Color Image (in this case only FITC and Cy3 are checked for Acquisition). 3) Select your new Microscope Configuration in the Configuration Drop-down button.