Microscope setup (TEM only)

Set up the microscope in scanning mode. Refer to your microscope manufacturer's user manual for details.

Configure the spectrum imaging technique

STEM SI TechniqueWithin the Gatan Microscopy Suite® (GMS) software, go to the Spectrum Imaging or STEM SI technique, then open the palettes you require for the experiment:

  • Scan – Controls the DigiScan™ system
  • SI Acquisition or STEM SI – Defines the spectrum imaging (SI) acquisition
  • Relevant signal acquisition palettes for each available signal
  • Additional data analysis palettes for the available signals
Note: By default, all signal acquisition palettes hide their respective Capture functionality. You can expand the palettes using the + icon to the right of the View button.

SI Acquisition or STEM SI palette

The SI Acquisition and STEM SI palettes enable set up and control of your SI experiment on the SEM and TEM, respectively. If no STEM SI experiment is currently set up, the palette appears in a mode selection state. Brief descriptions of the dialog features are given below.

In some models of the Monarc™ system, more than one acquisition mode is available within the SI workflow. In the CL palette, select the Spectrum or ARCL mode to collect a (wavelength) spectroscopy SI or an angle-resolved SI, respectively.

Signal selection

Signal selectionThe top section of the palette features a button for each available signal in the SI experiment (e.g., CL, EDS, EELS, and CBED) and an icon to allow simultaneous capture of other DigiScan signals (e.g., SE-BSE). For each signal selected, the appropriate acquisition palette automatically expands or collapses and may trigger requests to change the microscope state as necessary. At least one signal (in addition to the Scan button) needs to be selected, or the SI experiment cannot start.

Note: Some signals are mutually exclusive. Selecting such a signal will automatically deselect the other.

Mode selection

Use the palette's bottom section to set up the spatial coordinates of the SI. Pressing a mode button (2D Array, Line Scan, Multi-Point, and Time Series) will automatically assign a suitable survey image and create a default SI survey region of interest (ROI) marker on it. If no suitable image is available, a Preview type acquisition is automatically started and assigned.Mode selection

  • 2D Array – Regular 2D SI that consists of an array of equally spaced points in X and Y
  • Line Scan – 1D SI that includes an array of equally spaced points along a line
  • Multi-Point – Acquires a set of point spectra with identical parameters from individual spatial positions and collects them into a 1D SI data container
  • Time Series – Sequentially acquires a set of spectra with identical parameters from the identical sample area and collects them in a 1D SI data container

After choosing your signal and mode, a new palette is available. The palette includes:

  • Capture – Starts a new SI acquisition using the specified parameters
  • Pixel Time (s) – Specifies the beam's pixel dwell time and applies it to all spectral acquisition with the permitted values restricted to the minimum and maximum readout times of the selected detectors

Note: The acquisition time estimate automatically updates when you change the dwell time.

  • Live – Activates (blue) or deactivates (gray) live data display during SI acquisition
  • Drift – Activates (blue) or deactivates (gray) spatial drift correction

Mode specificsThe bottom parameters (boxed in portion of the image) dictate the specific modes of capture per the selection made in the STEM SI palette. The options available are dependent on the mode that was selected there; the options include:

2D Array

  • Size – Specify the size of the SI in pixels by using the Width and Height fields

The size automatically updates if you change the SI survey ROI position on the active survey image. When you change the Width value, it automatically adjusts the sampling resolution while keeping the acquired region the same. A change in Height changes the aspect ratio and hence the acquired region of the SI while keeping the sampling resolution identical.

Note: The acquisition time estimate automatically updates when the size is changed.

Line Scan

  • Line ScanSize – Specify the line scan Length in pixels

The sampling resolution automatically updates when the size is changed. Step displays the current sampling resolution in calibrated units. The SI size in pixels updates automatically when the sampling resolution is changed, keeping the acquired scan length identical.

  • Average dose – Enables the averaged line scan functionality and is not available for all systems and settings


  • Multi-PointNo. positions – Allows you to specify the SI size in number of individual positions

The number of survey ROI point markers is updated accordingly.

Note: You need to specify at least 2 points before the SI acquisition can start.

  • Arrange position – Click these buttons to arrange (selected) positions in various ways over the field of view

Time Series

  • Time SeriesRepeats – Allows you to specify the SI size in number of individual acquisitions

Note: You need to specify at least 2 repeats before the SI acquisition can start.

  • Delay (s) – Where you specify a pause in between two successive acquisitions

During these pauses, the signal controllers stop, and the beam control releases to the default. The acquisition is then in an idle state similar to a paused acquisition, but at the bottom of the STEM SI palette, it displays a countdown. At the end of the countdown acquisition, the next spectrum is automatically started.

  • 2D Scan – If left unchecked, the spectra will be acquired from a stationary position as indicated by an ROI point marker in the survey image

If checked, it acquires spectra while it rapidly and repeatedly scans a specified area. The ROI rectangle represents the area in the survey image and the two fields below the checkbox define sampling for this area. Enter values to change the area size or use the up and down arrows to change the sampling density of the area.