User and Configuration Settings

ScanImage® has 100s of settings that can be adjusted in its GUI windows. This state is represented as a set of properties, which can also be accessed/modified directly at the command line. For example the Zoom, Num Frames, and Pixels/Line values are all properties of the ScanImage® state.

When ScanImage® acquisitions are launched – by pressing one of the FOCUS, GRAB, or LOOP buttons in the Main Controls – the acquisition starts according to the current state ScanImage® properties.

The current state of ScanImage can be stored in Configuration and User Settings files. These files can later be loaded into ScanImage to restore a specific state.

General Rule


User Settings (USR)

Contains the ScanImage window layout, and general preferences.

Users typically save one USR file with their individual preferences

Window layout

Focus Duration

Configuration (CFG)

Contains experiment specific settings

Users typically save one configuration file per experiment setup

Zoom, Number of Frames, Pixels/Line

User Functions

Loading & Saving CFG & USR Files

The CFG & USR files can be loaded & saved from the Main Controls window


CFG & USR files are stored as binary MAT files

User Settings (USR) Files

USR files contain:

  • values of all properties in the User Settings windows

  • locations and visibilities of all the ScanImage® windows

  • a configuration (CFG) file to load when the USR file is loaded

When ScanImage® starts up, the user is prompted for a USR file which sets the default window locations/visibilities and loads the initial configuration (CFG) that the user prefers at the start of each ScanImage® session.

Configuration (CFG) Files

Users will typically have several CFG files. For example, a user may have one CFG file for collecting reference anatomical stacks slowly and another for fast functional imaging with USR settings.

The User Functions settings are among the Configuration settings. These can be used to customize ScanImage® operation according to user developed scripts and specified arguments.

Because User Function settings are tied to specific CFG files, users can readily switch between default and user-customized ScanImage® operations by switching their CFG files.

For the fastest experimental workflows, Fast Configurations can be used to switch CFG files at the touch of a single button.