In the scanning (SEM), and scanning transmission electron microscope (STEM) mode in a TEM, the electron beam is focused on a small probe and rastered to acquire spatial information in a serial manner (X, Y). In the wavelength-filtered spectrum image (SI) mode, it collects the wavelength information (λ) serially, e.g., captures a series of (aligned) wavelength-filtered maps over a defined spectral range (or ranges).

A typical workflow includes:

  1. Set up the microscope in scanning mode and in the appropriate spectrometer state that you wish to use (TEM only).

  2. Ensure that the region of interest is viewable within a DigiScan™ survey image.

  3. Define the wavelength range and sampling rate to collect the SI.

  4. In the Scan Setup dialog, specify which signals you want to acquire.

  5. In the Scan Setup dialog, specify the pixel density and dwell time you want to use.

  6. Select Capture on the Wavelength Filtered SI palette.

Here are detailed SI workflows you can follow to better understand your sample when you use Gatan Microscopy Suite® software.

Wavelength Filtered SI setup

Microscope setup (TEM only)

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

Within the Gatan Microscopy Suite software, go to the CL Imaging technique, then open the palettes you require for the experiment:

  • CL Imaging – Controls the CL spectrometer

  • Scan – Defines setting for the DigiScan™ system

  • Wavelength Filtered SI – Adjusts the wavelength range and sampling

CL Imaging

Select WL Filtered mode to designate enable the wavelength-filtered functionality.


Select the Setup icon to access the DigiScan Setup dialog and define the signal parameters you want to collect, including the image width and height (pixels), plus pixel time of the individual wavelength-filtered images. We recommend capturing at least one additional signal to the CL signal. 

Wavelength-filtered SI

Define one or more wavelength ranges by entering the Begin WL (nm) and End WL (nm) wavelengths into the table. Enter the values by selecting the + icon and completing the dialog. You may edit entries in the table by double-clicking on a value and overwriting the entry. Or you can highlight a row, then select the X icon to delete the entry.   

Flow control


Once the SI acquisition parameters are set up, select the Capture button on the Wavelength Filtered SI palette to start the acquisition.

Once selected, the SI acquisition routine will take control of the microscope beam and begin the acquisition. During acquisition, the Capture button pulses in blue to indicate that an acquisition is in progress. When in this state, a subsequent click of the Capture button halts the acquisition. While the acquisition proceeds, Gatan Microscopy Suite displays a new workspace and fills it with image stacks for each of the DigiScan signals you request.

Note: During active SI acquisition, the spectrometers in use are not available for single spectrum acquisition.

You can monitor how the acquisition is proceeding using the Visual Feedback provided. Each SI is displayed in a new image window, which fills as the acquisition proceeds. If at any point you wish to halt the acquisition, click on the pulsing Capture button. When the acquisition halts or completes, the beam control returns to the Beam Safe Point (if one is defined) or returns to the microscope.

After the acquisition

We recommend that you immediately save all data before analyzing and/or removing artifacts.

Artifact removal


By using the Image Processing technique, you can calculate and eliminate inter-frame drift from the data cube. Specifically, you can use the Image Alignment palette to align a series of images to one another or to images in another series. This is an essential step before analyzing wavelength-filtered SIs.

The image alignment process and drift removal are documented in the help files of Gatan Microscopy Suite software.

Spectrum Image analysis

For more details on the analysis of the spectrum image data cubes that are collected by wavelength-filtered spectrum imaging please refer to the Analyze section, in particular, the linear least squares fitting discussion.