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3D Tomography Acquisition Software


3D Tomography Acquisition

For tomographic tilt series acquisition (TEM, STEM & EFTEM)

Electron tomography is a method for determining 3D structures. Gatan’s 3D Tomography Acquisition Software acquires a series of projections using your electron microscope, tilting the sample by a small increment between each projection. Gatan’s 3D Reconstruction Module can then be used to align the data and generate a 3D volume.


  • Live tracking and stage calibration methods to track specimen drift and stage movement
  • Manual override mode for excessively low contrast samples and poor stages
  • Tracking data can be used to reduce dose on future acquisitions and improve tracking at high magnification
  • Intelligent prompting when there is too much drift


  • Tracking data and stage calibration reports
  • Log of corrections applied as the series acquisition progresses
  • Summary of experiment set-up from tilt series

2D Visualisation

  • Step through the series of images and examine individual planes
  • Play the tilt series as a video, which can be exported


  • Compatible with a wide range of microscopes with computer-controlled stages.

Contact us for more information and quotes:
+44 (0)1223 422 269 or info@blue-scientific.com

Gatan 3D Tomography Acquisition Software

STEM Image of a GaN Nanowire

STEM tilt series image of GaN nanowire. Courtesy Dr. Ilke Arslan, Sandia National Laboratories, California.


  • Life science
  • Material science
  • Natural resources
  • Electronics


  • Features to overcome common problems of drift and poor overlaps
  • Acquire TEM, STEM or EFTEM images
  • Export data in various formats
  • Compatible with most TEMs with computer-controlled stages

TEM Tomography

Collect data in TEM mode using any microscope.

Drift correction is performed using the objective lens and image-shift, beam-shift deflectors.

  • Compatible with all Gatan digital cameras
  • Z-tracking through beam-tilt induced image-shift method

Computer-controlled hardware required:

  • Objective lens
  • Image-shift deflectors
  • Beam-shift deflectors
  • Tilting stage

STEM Tomography

Collect data in STEM mode on your microscope.

  • Use with a wide range of DigiScan compatible STEM detectors
  • New Z-tracking algorithm for better than one nanometre accuracy, suitable for precipitates, nanowires, calibration gratings and more
  • X and Y drift correction with sub-pixel accuracy
  • Focus automatically adjusts throughout the acquisition series
  • Independent magnification levels for tracking and data acquisition
  • Simultaneous STEM signal acquisition eg bright and high angle annular dark field signals

Computer-controlled hardware required:

  • Condenser and/or objective lens
  • Tilting stage
  • DigiScan scan generator
  • Compatible STEM detector

STEM Tomography - Dynamic Focus

Gatan software features dynamic focus for STEM images, which adjusts focus throughout the series for sharper images.

EFTEM Tomography

Collect data from your TEM equipped with an energy filter. This is the only commercial software available for EFTEM tomography.

  • Track X,Y and Z drifts at any energy loss or with zero-loss or unfiltered images
  • Periodically adjust the filter to correct energy drift (Gatan imaging filters only)
  • Perform jump-ratio, elemental and thickness mapping

Computer-controlled hardware required:

  • Gatan imaging filter or certain other in-column filters together with a Gatan CCD camera
  • Objective lens
  • Image-shift deflectors
  • Beam-shift deflectors
  • Tilting stage

EFTEM Tilt Series

EFTEM tilt series of carbon nanotubes containing iron catalyst particles with TiO2 powder. Acquired using the Gatan GIF Tridiem energy filter.


3D Tomography Videos