Spectrum Imaging

To enhance your spectroscopy and mapping experiments, use the Spectrum Imaging (SI) mode to collect and store three-dimensional data that contains spatial and spectroscopy information together. Or, to extend your angle-resolved analysis of a sample’s emission pattern, you can use the SI mode to collect and store four-dimensional data that contains spatial and angular information.

Wavelength-Filtered SI

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. 

Wavelength/Angle-Resolved SI

The spectrum imaging (SI) technique is useful to collect either wavelength-resolved spectrum images or (angle-resolved) emission pattern images.

The electron beam is focused into a small probe and rastered to acquire spatial information in a serial manner (X, Y). In SI acquisition mode, you acquire a spectrum (or emission pattern) at each pixel position, hence build up the spectrum image on a spectrum-by-spectrum or emission pattern-by-emission pattern basis. A typical workflow includes:

  1. Set up the microscope in scanning mode and in the appropriate state for the spectrometer you wish to use.

  2. Use the DigiScan™ system to acquire and assign a survey image.

  3. Create a spectrum image survey region of interest on the survey image.

  4. View the spectrum/emission pattern from the region you wish to acquire the spectrum image from.

  5. In the SI Setup dialog, specify which spectrum signals you want to acquire.

  6. If artifact corrections are required, enable them and/or create the artifact correction survey regions of interest.

  7. In the Spectrum Image dialog, specify the pixel dwell time you want to use and the size of the spectrum image in pixels.

  8. Select Start on the Spectrum Imaging dialog.

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


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.

Survey Image

Each spectrum image acquisition requires a survey image. It provides a frame of reference and serves as a useful reminder of where the data was acquired. You can only assign one image at a time as the active survey image. This image should be recently acquired and of good quality. Images acquired with too short a pixel dwell time can result in inaccurate beam positioning and a mismatch of indicated and acquired spectrum image position. The survey image can be either a recently acquired (static) image, or a still continuously acquiring image. For a beam sensitive specimen, a recently acquired image might work better. Whereas a continuously acquire image can be beneficial to avoid charge-induced specimen drift at high magnification and to provide the most accurate survey image at the start of spectrum image acquisition.

Collect and assign a survey image

  1. Locate the region of the sample you are interested in.

  2. Collect an image.Collect an image.

Use a dwell time of 16 μs/pixel or longer. The long dwell time ensures an accurate microscope beam position in subsequent analysis. Make sure that the region you wish to acquire is smaller than the field of view, typically about one-third of the size. This allows the beam deflectors to correct for spatial drift and also ensures that the spectrum image (SI) region is well represented in the survey image.

  1. Select a SI mode or use the survey region of interest (ROI) tool from the floating menus over the image.

Either action automatically assigns the frontmost image as the survey image. The window title changes to remind you that this is now the current survey image.

  1. Refresh the survey image.

The current survey image is automatically de-assigned when a different survey image is selected. If you close an active survey image or remove all survey ROIs, the STEM SI palette reverts to the mode selection state.

When a SI is acquired, it creates a copy of the survey image on the SI data workspace. This image acts as data reference, which causes the survey ROI to no longer be moved or resized. Only the survey image on the View workspace is actively linked to the SI palette and interactive.

Select and Survey ROI

For a spectrum image (SI) acquisition, it is necessary to allocate a region on the survey image to use for acquisition. A green region of interest (ROI) marker identifies these regions. The type of the SI marker depends on the SI mode and can be either point, line, or rectangle ROIs. You can position, resize, and remove the survey ROI like any other ROI marker.

  1. Add a survey ROI by selecting a SI mode.

If the SI palette is in mode selection state, selecting any mode automatically adds the appropriate survey ROI to the survey image, which is also automatically assigned by this action. The position and size are the same as the one used for the last SI acquisition of that type.

  1. Add a survey ROI by using the floating menu.

When you right-click a recent image on the View workspace, the SI ROI tool in the floating menu appears. This dropdown menu allows you to select the SI type. With this tool, you can create the survey ROI directly on the image. Then, the image is automatically assigned as a survey image while the spectrum imaging mode is adjusted. Other, now obsolete survey ROIs are automatically removed.

Note: For Multi-Point, keep the Shift key pressed while adding a point to keep the tool active and allow the selection of multiple points in a series of clicks.

  1. Remove a survey ROI.

Use the mouse to click the ROI marker while you press the Delete key on the keyboard. If you remove all survey ROIs of the current SI mode, the STEM-SI palette automatically reverts to mode selection state.

Survey ROI types

2D Array

A regular 2D SI consists of an array of equally spaced points in X and Y. It is represented as a single, rectangle ROI in the survey image.

Resizing the survey ROI keeps the total number of pixels and hence total acquisition time approximately constant. The SI size in pixels, as well as the sampling resolution, change automatically when you resize the ROI.

The survey ROI snaps to positions of the appropriate size and aspect ratio. The smaller the total number of pixels in the SI, the rougher those snaps may appear.

Line Scan

A one-dimensional (1D) SI consists of an array of equally spaced points along a line. It is represented as a single, line ROI in the survey image. A yellow cross indicates the start position of the scan. If the averaging option is enabled, the cross is replaced by a yellow line that indicates the averaging direction and width.

Resizing the green survey ROI adjusts the sampling resolution, but keeps the number of sampled points constant. Changing the dimensions of the yellow survey ROI adjusts the averaging width, but keeps the number of sampling points along that direction constant. You can adjust the averaging direction angle by pressing the Ctrl key down while you drag the green handle of the yellow survey ROI. Deleting the yellow survey ROI will switch the averaging option off.


A set of point spectra acquired with identical parameters from individual spatial positions collected in a 1D SI data container. Each point is represented by a single, numbered point ROI in the survey image. This number specifies the spectrum position within the SI data container.

It is most convenient to add points using the SI ROI tool from the floating menu. Keeping the Shift key pressed allows you to add multiple points in a series of mouse clicks. You can remove individual points by selecting them and pressing the Delete key. Once deleted, this automatically renumbers the remaining points.

Click the Arrange points buttons to arrange the selected set of points or if none are selected, all points. If a rectangular ROI is selected, it arranges points within this area. Otherwise, it arranges them over the entire survey image.

Auto arrange points
Selection of points and destination area (left). Randomize positions in the area where each point is given an arbitrary position within the area (right).

Auto arrange points
Arranged points along a regular grid (left). Arrange point along a regular grid, but randomize around this position (right).

Time Series

A set of spectra sequentially acquired with identical parameters from the identical sample area collected in a 1D SI data container. The sample position is either represented by a point ROI for stationary acquisition or by a rectangular ROI if the 2D Scan option is enabled.

Resizing the 2D Scan area is restricted by the number of sampling points of the scan, which in turn is limited by the SI Pixel Time. Slower scans allow a higher sampling. To access a larger scan area, it can, therefore, be necessary to either reduce sampling with the spin controls for the 2D Scan fields and/or to increase the Pixel Time.

Flow Control


Once the spectrum image (SI) acquisition parameters and any artifact corrections are set up, select the Capture button on the SI palette to start an acquisition. If you wish to update the survey image before proceeding with acquisition, right-click on it and select Restart scan from the context menu.

Once started, the SI acquisition routine will take control of the microscope beam, and the acquisition then begins. During acquisition, the Capture button pulses in blue to indicate that an acquisition is active and that a subsequent click of the Capture button halts acquisition. A new workspace is created and filled with a copy of the survey image and data containers for all acquired signals.

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

If spatial drift correction is enabled, then some preliminary measurements are performed. Visual feedback on the measurements may be provided, depending on the preferences specified.

You can monitor how the acquisition is proceeding using the visual feedback provided. Each SI displays in a new image window, which fills as the acquisition proceeds. Live spectra may also be shown or hidden as desired. If you wish to halt the acquisition, click on the pulsing Capture button. When the acquisition is halted or completes, the beam control returns to the Beam Safe Point (if one has been set up), or alternatively, it is returned to the microscope.


During a SI acquisition, it may become necessary to perform a microscope adjustment that temporarily degrades the data collected by the spectrometer. At such times, you should pause the acquisition, carry out the adjustment, and resume after conditions have stabilized. To pause the acquisition at any time, click on the pulsing Capture button in the STEM-SI palette while keeping the Alt key pressed at the same time—the label of the Capture button changes to Resume.

When you pause the acquisition, the beam either moves to the Beam Safe Point (if you defined one) or returns otherwise beam control to the microscope. If the acquisition is paused and restarted, the software immediately carries out spatial drift corrections if you enable Apply on Resume from Pause, before continuing to acquire data from where it was before the pause.

To resume acquisition from the paused state, click the Resume button. To stop acquisition from the paused state, click on the Resume button while pressing the Alt key at the same time.

Note: Pausing is not available for hardware synchronized acquisitions. On systems which by default use hardware synchronized acquisition, you can force software synchronization via the Setup dialog.

After the acquisition

If the autosave functionality is enabled, all experimental data is saved immediately using the current SI group saving options. If the close column values after acquisition option is enabled, the microscope column valves are closed (on systems that support column valve access). You can use the (still) active survey image on the View workspace to immediately restart an identical or similar acquisition after adjusting survey ROIs and parameters.

Visual Feedback

Spectrum image display

During spectrum image (SI) acquisition, it shows each SI in its own image display. The spectrum image fills as the spectral data is acquired and placed into position in the SI. You can use the 3D visualization tools to explore the spectral data while the acquisition is running (e.g., Slice tool). Since there is a processing overhead that may introduce artifacts into your data acquisition, we advise doing this after acquisition or while paused.

Live spectra

Live spectral feedback during acquisition can be enabled or disabled with the Live button in the STEM-SI palette. You can manipulate the live spectra using the standard tools for line plot display visualization.

Live spectra

Beam position cursorBeam position cursor

During acquisition, an orange beam cursor marks the beam position on the survey image. This indicates the progress of the acquisition, and its position may vary slightly from that of the beam. For particularly fast acquisitions, the cursor is displayed as a line or even completely disabled.

Pixels per second

Pixels per secondThe actual SI acquisition rate is posted to the Gatan Microscopy Suite® software status area at the bottom of the application. It displays in units of pixels per second. This information can be useful when you configure a spectrometer for optimal readout speed.

Time remainingTime remaining

The remaining acquisition time is displayed in real-time in the STEM-SI palette just above the Capture button. This time is based on the actual acquisition rate, excluding any pauses.


Spatial drift correction

Thermal effects and mechanical instabilities in the microscope can cause the sample to drift under the electron beam. Since the acquisition of a spectrum image (SI) can occur over a considerable period, this drift could easily cause features to smear in the SI. Indeed, SI acquired over a long time at high magnification may contain data from a much different region of the sample than desired. Spatial drift is worse at higher magnifications and varies from one microscope to another and even from one microscope session to another.

Spatial drift correction entails a cross-correlation of a reference region with a new scan of the same region taken periodically throughout the acquisition of the SI. The cross-correlation process works better if there is some unique spatial structure in this spatial drift region.

First, define a region to perform a reference scan on the survey image. At the start of the SI acquisition, it takes the first drift measurement scan from the same region and corrects for any spatial drift. The scan resolution and pixel dwell time used for the spatial drift scans are the same as for the survey image. Drift is measured by cross-correlation; thus the correction is applied as an offset to the beam scan coordinates. When you take a measurement, the data posts to the Gatan Microscopy Suite® software results window. If the survey image is calibrated, it quotes any shift in calibrated units. During acquisition, the drift measurement repeats periodically using the specified frequency. After the acquisition, you can view the drift measurement using the Show correction menu item in the SI menu.

Note: Since the drift image is acquired during the SI acquisition, the detector must not interfere with the spectrum acquisition when inserted.

Set up for spatial drift correction

  1. Acquire a survey image and assigned it for the SI acquisition.
  2. Activate the Drift button on the STEM-SI palette.

A rectangular region of interest (ROI) marker labeled Spatial Drift shows on the survey image, indicating the measurement area for drift correction.

  1. Adjust and accept the correction frequency settings.

Frequency optionsThe optimum frequency of corrections depends on the magnitude of the drift. It is a compromise between keeping the total acquisition time short and getting clean SI data. When you choose a drift correction frequency based on spatial features (pixels, rows, frames), this generally gives a more pleasing result than the time-based settings.

  1. Adjust the Spatial Drift ROI.

Adjust the spatial drift ROIUse the mouse to resize and move the ROI to an appropriate location. The measurement area should be at least twice as big as the maximum drift expected in between two subsequent measurements. It should contain an easily recognizable feature of sufficient contrast. Ideally, the area should not overlap with the data acquisition area.

  1. Adjust the advanced drift correction options (if needed).

Click the Drift button while pressing the Alt key to directly access the drift correction options page of the Spectrum Imaging Setup dialog.

Viewing point spectra

When configuring the various spectrometers for SI acquisition (e.g., determine the optimum pixel dwell time for acquisition), it is often desirable to acquire a continuous spectrum from a region in the survey image. The microscope beam can be placed anywhere within the survey image using the Spot functionality so you can view the spectrum from each spectrometer at that position.

Viewing point spectra

To view the spectrum at a particular point:

  1. Acquire and assign a survey image.

  2. Enable the Spot button the Scan palette.

A cursor labeled Beam appears on the survey image. If the survey image is currently acquiring, the marker is labeled Park instead. In this case, stop the acquisition to get a stationary beam.

  1. Start a continuous acquisition from the spectrometer(s) of interest using the View button of the respective Spectral Acquisition palette – The spectrum acquisition appears in a new line plot image display.

  2. Drag the beam cursor around to view the spectrum at various points.

The spectrum display continues to display data from the spectrometer as the spot marker tool moves around. Use this mode to establish the optimal acquisition parameters for SI acquisition.

Beam safe point

Beam safe pointWhen the acquisition is paused or has finished, an attempt is made to minimize possible beam damage to the specimen. The beam either moves to the park point (if you have defined one) or the beam control returns to the microscope.

Note: The point is labeled Park during an active scan. This label name changes to Beam while no scan is active and the beam is stationary at the indicated location.

To set up a safe point:

  1. Ensure a survey image is assigned.

  2. Enable the Spot mode on the Scan palette, and position the beam cursor at the safe point – A region in the vacuum is ideal.

  3. If the SI acquisition pauses, or when the acquisition terminates, the beam returns to this point.

Advanced SI

Once acquired, you can treat a cathodoluminescence (CL) spectrum imaging (SI) dataset I(λ,x,y) or I(θ,Φ,x,y) as a collection of spectra or sequence of images irrespective of acquisition mode. You can apply conventional CL processing techniques or progress to use more advanced analysis techniques. 

For more information, see the Analyze section.