Optimize Maps

EFTEM mapping is generally limited by three effects:

  • Shot noise

    • Symptom – Noisy maps especially in areas that should have high, uniform composition of the element; results from the inherent statistical variation in the arrival rate of electrons on the detector

    • Solution – Acquire more electrons per pixel; typically you optimize a combination of beam current, exposure time and binning

  • Chromatic aberration

    • Symptom – Fringes along boundaries that separate dark and bright parts of the image; typically occurs when you do not use an objective aperture

    • Solution – Reduce the slit width and objective aperture to minimize the effects of chromatic aberration; however, this will reduce the number of electrons collected and increase the shot noise

  • Image drift

    • Symptom – Unidirectional fringes along interfaces that separate dark and bright parts of the image and in areas with a lot of diffraction contrast

    • Solution – Repeat the drift correction function with different parameters or in manual mode; ensure the sample is not damaging or shrinking; reduce exposure time and/or increase beam intensity

  • Image focus

    • Symptom – Blurred EFTEM maps at an energy loss

    • Solution – Focus the image 

There are a number of general parameters you can choose to further optimize your EFTEM maps when you use Gatan Microscopy Suite® (GMS) software. These parameters affect all EFTEM acquisition modalities (e.g., SingleMap, MultiMap) and you can locate them in the EFTEM Mapping Preferences dialog.

  1. Go to the EFTEM palette, then click the Setup button.

  2. The EFTEM Mapping Preferences dialog will then open.

Drift measurement

During EFTEM data acquisition involving multiple images (e.g., summed image acquisition or mapping using multiple windows) the sample may drift, resulting in a spatial mismatch between images acquired successively. If not accounted for, this spatial mismatch will introduce artifacts into the final map or image. The EFTEM mapping routines have drift correction procedures that you can configure via the Drift Correction tab located in the EFTEM Mapping Preferences dialog.

  • Plane-to-plane alignment – Post-processing steps that correct drift between successive energy integration ranges in an EFTEM acquisition

  • Cumulative alignment – Fully automates drift correction during a cumulative (or summed) acquisition between successive planes at the same energy integration range

Map computation

The parameters set here globally affect how you perform map computations.

  • Automatically remove x-rays – Replaces erroneously high or low values in the source images with their local neighborhood average prior map computation

  • Hole-count threshold – Treats values below the set threshold as zero and omits them for the computation of maps; these typically are holes in the sample (e.g., regions with no sample)

  • Background model – Specifies the elemental mapping model you will use to compute the post-edge background contribution from the pre-edge images during creation of a 3-window elemental map


When MultiMap is present, the Options tab is available. It contains the options which will globally affect all MultiMap acquisitions.

  • Colorize thickness map – When this option is selected the thickness map will be colorized
  • Automatically save and organize maps – Mapping routines will automatically save all acquired images at the end of acquisition using the Group Save options

Auto Exposure

The Auto Exposure dialog contains a fast and robust auto-exposure and -binning routine to help simplify the acquisition of elemental maps with optimal image intensity. The behavior of the auto-exposure and -binning routines is dependent on both the preferences you specify as well as on the particular acquisition type.

  • Exposure – Sets the minimum and maximum exposure times the auto-exposure routine uses for EFTEM single and multi-mapping

  • Intensity – Determines the target intensity the auto-exposure routine will aim for, along with the minimum and maximum acceptable limits

  • Binning – Allows charges from adjacent pixels to be combined to increase readout speeds

Note: You can use Binning to trade signal-to-noise ratio (SNR) for a number of pixels. Fewer pixels (higher binning) gives better SNR, but lower resolution. Typically 2x or 4x is used for edges up to 1 keV and 4x or 8x is used above 1 keV.

Energy offset method

The EFTEM modes adjust the TEM high voltage to offset the energy during acquisition. This helps ensure the lower column and the GIF remain in focus and aligned throughout the experiment. The other methods of offsetting the energy are used for spectroscopy and are described here.

Note: EFTEM at high energy losses is an incoherent imaging process. Conventional bright-field TEM imaging is a coherent imaging process and lens defocus is used to add contrast to the image (for example Scherzer focus is typically used for HREM imaging). Incoherent images are only sharp for one value of focus (Gaussian focus). In addition, the large angular distribution of the energy loss electrons results in a very narrow depth of focus. This makes focusing at a reasonable large (~400 eV) energy loss prior to the start of acquisition critical for EFTEM mapping. Since the high voltage offset is used in EFTEM acquisition and the energy of the detected electrons stays fixed, once the Gaussian focus is found, the focus does not need to be changed when the energy offset is changed.


Berger, A.; Kohl, H. Optimum imaging parameters for elemental mapping in an energy-filtering TEM. Optik. 92:175 – 193.

Kothleitner, G.; Hofer F. Optimization of the signal to noise ratio in EFTEM elemental maps with regard to different ionization edge types. Micron. 29349 – 357; 1998.