Scanimage 2017 : Setting Up ScanImage


Here we'll review the bare minimum to get a system up and running.

Software Requirements

Start by installing required software and hardware.

Install ScanImage

  1. Download the ScanImage Installer.
  2. Run the installer and complete all steps (be sure to select all releases of MATLAB that you want ScanImage installed to).
  3. Start MATLAB. If MATLAB was already running, restart it.



While using the installer is recommended, if you want more control over where ScanImage is installed, you can manually install ScanImage from the zip download.

Start scanimage

  1. Launch the Matlab application.
  2. In the Matlab command window, type:

  3. If this is the first time scanimage is run, see Machine Data File (MDF) section, below.
  4. The ScanImage Configuration dialog appears.

  5. Browse to the folder that contains your Machine Data File (MDF).
  6. Press Continue.

    (tick) To run scan image, make sure your Digital IO Device is connected to your system and is turned on before you start your computer.


Machine Data File (MDF)

If the is first time you are running ScanImage, the following ScanImage dialog box will appear:

  1. Press 'Create..'. 
    1. A Machine Data File is created.

  2. Locate and Save the Machine Data File in a location that is backed up.

    (tick) Recommended location for the Machine Data File is a folder named 'config'  at  root of the user's Data directory. In the example above, 'E:\' is backed up, thus, the Machine Data File in the 'config' folder is backed up. 

  3. The system launches the ScanImage Machine Configuration Editor to setup your microscope configurations.
    The first time this configuration application is launched, it acts like a setup wizard, taking you step-by-step through your configuration.
    Subsequent settings can be added and update after the initial installation by accessing the  ScanImage Machine Configuration Editor through the Main Controls, File Menu, Machine Configuration... option.

  4. When you reach the following screen, you can either press "Finish and Run ScanImage" or continue with additional machine setup options.

  5. A Machine Data File  (MDF) will be created and the ScanImage application will be launched.

    (tick) The Machine Data File (MDF) contains information used to describe aspects of the hardware configuration that rarely change.  The contents of the MDF is accessed and applied at the startup of ScanImage. Any change to the MDF during an experiment requires a Matlab restart.

USR/CFG Settings

Additional hardware configuration and window position information is stored in the USR file.

On the first startup, you may be prompted to locate the USR File.  Hit Cancel to proceed using default settings.

After starting ScanImage successfully, you should soon thereafter arrange windows as you prefer them and then save a USR file via the File >> Save User Settings As... menu item on the Main Controls. Later, select this USR file to use the saved settings.