Microscope setup

Set up the microscope in scanning mode and in the appropriate state for the spectrometer you wish to use. Refer to your microscope manufacturer's user manual for details.

Enter and configure the STEM SI technique

STEM SI TechniqueWhen you configure your system for STEM spectrum imaging (SI) acquisition, you can control your STEM SI easily when you use Gatan Microscopy Suite® (GMS) software.

In the home Techniques Manager, select the STEM SI button to open the STEM SI technique palette, which contains everything that is required for the experiment:

  • Scan palette to control the DigiScan™ system

  • STEM SI palette to set up the STEM SI acquisition

  • Relevant signal acquisition palettes for each available signal

  • Additional data analysis palettes for the available signals

Note: All signal acquisition palettes hide their respective Capture functionality by default. You can expand the palettes using the plus icon to the right of the View button.

STEM SI palette

Setup and control of the SI acquisition is provided via the STEM SI palette. On the initial display, or if no STEM SI experiment is currently set up, the palette will be displayed in mode selection state. Brief descriptions of the dialog features are given below.

Signal selection

Signal selectionThe top section of the palette features a button for each available signal in the STEM SI experiment (EELS, EDS, CBED, and CL). The according signal acquisition palette will be automatically expanded or collapsed which may trigger requests to change the microscope state if required. At least one signal (in addition to the Scan button) needs to be selected or the SI experiment cannot be started.

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

Mode selection

Mode selectionUse the bottom section of the palette 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 ROI marker on it. If no suitable image is available, a Preview type acquisition is automatically started and assigned.

  • 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 – Set of point spectra acquired with identical parameters from individual spatial positions collected into a 1D SI data container

  • Time Series – Set of spectra sequentially acquired with identical parameters from the identical sample area collected in a 1D SI data container

After choosing your signal and mode, a new palette will be available. The palette will include:

  • Capture button – Starts a new SI acquisition using the specified parameters

  • Pixel Time (s) – Specifies the pixel dwell time of the beam and will apply to all spectral acquisition with the permitted values being restricted to the minimum and maximum readout times of the selected detectors

Note: The acquisition time estimate is automatically updated when the dwell time is changed.

  • Live button – Activates (blue) or deactivates (gray) live data display during SI acquisition

  • Drift button – Activates (blue) or deactivates (gray) spatial drift correctionMode specifics

The 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 will automatically adjust the sampling resolution while keeping the acquired region the same. A change in height will change 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 checkbox – 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 region of interest (ROI) point markers is updated accordingly.

Note: At least 2 points have to be specified before SI acquisition can start.

Arrange position buttons – 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: At least 2 repeats have to be specified before SI acquisition will start.

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

During these pauses, signal controllers are stopped and the beam control is released to the default. The acquisition is then in an idle state similar to a paused acquisition, but a countdown is displayed at the bottom of the STEM SI palette. 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, spectra are acquired while a specified area is rapidly and repeatedly scanned. The area is represented by an ROI rectangle in the survey image and sampling for this area is defined by the two fields below the checkbox. Enter values to change the area size or use the up and down arrows to change the sampling density of the area.