3D Tomography-Acquisition Software

A Complete Solution Integrated in DigitalMicrograph

TEM Tomography, STEM Tomography, and EFTEM Tomography software

Electron tomography has become a popular means to determine three dimensional structures on a range of scales in materials ranging from biological samples to those typical of the semiconductor industry. These diverse specimens, however, require a diverse number of techniques to best understand the material under study. Gatan now provides tomography acquisition software in DigitalMicrograph™ that makes it possible to collect a tomographic tilt series using TEM, STEM or EFTEM modes of operation.

TEM Tomography in DigitalMicrograph. Gatan’s 3D Tomography Software collecting a tilt series from a sample of boron nanotubes. The three images on the top right show the focus tracking in progress, while the three images on the bottom right show the x,y tracking in progress. The large image on the left displays the collected tilt series. The palette on the top right shows the tomography control interface.

Tomography Software Features

Whether you collect your data in TEM, STEM or EFTEM mode the software provides the following key features:

Tracking
• Live tracking or Stage Calibration methods for tracking specimen drift and stage movement.
• Manual override mode for extreme low contrast specimens or particularly a poor stage.
• Tracking data can be used to reduce dose on subsequent acquisitions or to improve tracking at high magnifications.

Report Generation
• Graphical output of tracking data measured during series acquisition.
• Graphical output of stage calibration used, or stage calibration for current holder.
• Log of corrections applied as series acquisition proceeds.
• Summary of experiment setup from tilt series.

2D Visualization
• Step through acquired series and view individual planes.
• Play tilt series as a movie and export to movie format.

Data Access
• During acquisition data can be saved plane-by-plane to file or stored in memory, or both.
• 3-D series can be saved in DM3 or other formats for import into other reconstruction and visualization packages.
• Access data through DigitalMicrograph’s powerful scripting language.

Compatibility
• The Gatan Tomography software is compatible with a broad range of microscopes equipped with computer controlled stages – see the particular mode of interest for further details.

TEM Tomography

The TEM Tomography software enables collection of data in TEM mode on any microscope equipped with the following computer controllable components:
objective lens, image-shift deflectors, beam-shift deflectors, and a tilting stage. Drift corrections are performed by means of the objective lens and image-shift, beam-shift deflectors. Specific features are:

• Supports any Gatan digital camera
• Tracking can be performed using Live Tracking, Stage Calibration, or both
• X,Y and Z stage tracking and correction with sub pixel accuracy
• Intelligently requests user for “manual assist” if problems arise

STEM Tomography

• Supports a wide range of DigiScan compatible STEM detectors
• Tracking can be performed using Live Tracking, Stage Calibration, or both
• Novel Z tracking algorithm tested successfully on precipitates, nanowires, calibration gratings and more with accuracy to better than one nanometer
• X and Y drift correction with sub pixel accuracy
• Focus dynamically adjusted through acquisition of each image to ensure focus on tilted specimens
• Independent magnification levels for tracking and data acquisition
• Simultaneous STEM signal acquisition – e.g. bright field and high angle annular dark field signals
• Intelligently requests user for “manual assist” if problems arise

Click on the image above to play the movie. If you have a problem viewing these movies click here to download the BF movie (left) and here to download the HAADF movie (right). Interplanetary dust particle. STEM tilt series acquired with a Gatan 805 BF/ADF detector and Gatan 806 HAADF detector from -61° to 68° by Dr. Ilke Arslan of Sandia National Laboratories, Livermore, California and Dr. John P. Bradley of Lawrence Livermore National Laboratory, Livermore, California.

EFTEM Tomography

The ETEM Tomography software enables collection of data from a microscope equipped with an energy filter. The filter can be either a Gatan Imaging Filter or certain JEOL or ZEISS in-column filters with a Gatan CCD camera. The microscope must be equipped with the following computer controllable components: objective lens, image-shift deflectors, beam-shift deflectors, and a tilting stage. Specific features are:

• The only commercial software which enables EFTEM Tomography
• Acquire an EFTEM tilt series on a TEM equipped any energy filter (Gatan Imaging Filter or an in-column filter) and a Gatan Camera
• Tracking can be performed using Live Tracking, Stage Calibration, or both
• X,Y and Z stage tracking and correction with sub pixel accuracy
• 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 (available on Gatan Imaging Filters only)
• Full support for jump-ratio, elemental or thickness mapping
• Intelligently requests user for “manual assist” if problems arise

Click on the image above to play the movie. If you have a problem viewing this movie click here to download a copy. Carbon nanotubes containing iron catalyst particles with TiO2 powder. EFTEM tilt series acquired with a Gatan Tridiem energy filter from -50° to 50°. A plasmon series (5eV slit, 17.6eV energy), titanium L-23 series (30eV slit, 2 pre-edge, 1 post-edge), and  iron L-23 series (40eV slit, 2 pre-edge, 1 post-edge) were collected. Elemental series for titanium (blue) and iron (red) were generated with Gatan’s elemental mapping software and combined with the plasmon series (green).

3D Reconstruction

The Gatan Reconstruction Software provides tools to precisely align the 2D projections collected by the Tomography Software and generate a 3D volume from the aligned projections. It is strongly recommended that this software be run on a system with at least 2GB of RAM. Specific features are:

• Manual and Automatic tilt series alignment with sub-pixel accuracy
• Manual and Automatic determination of tilt axis location
• Multiple reconstruction algorithms including Weighted Back Projection (WBP) and the Simultaneous Iterative Reconstruction Technique (SIRT)
• Memory conserving version of the WBP and SIRT Algorithms available
• Support for sub-volume reconstruction
• Live updates of volume during reconstruction

Comparison of reconstruction algorithms from simulated data. The left image shows the original object, a cube. Projections were generated from -60 degrees to +60 degrees at 1 degree intervals. The middle image shows the cube reconstructed using weighted back projection. The right image shows the reconstruction using 20 iterations of the SIRT algorithm. The blue and red levels correspond to 30% and 60% of the maximum level in the reconstruction.

3D Visualization

The Gatan 3D Visualization Software enables the viewing and interpretation of reconstructed 3D volumes. It is strongly recommended that this software be run on a computer equipped with a ‘high-end’ graphics card (NVidia or ATI) and at least 2 GB of RAM. Specific features are:

• Fully interactive and integrated with DigitalMicrograph
• Memory Efficient Volume rendering
• Memory Efficient Isosurface rendering
• Orthogonal slicing
• 3D line profiles
• 3D ROI specification and extraction
• Simple Movie export (MPEG, AVI)

Image of interplanetary dust particle; STEM tilt series acquired with a Gatan 806 HAADF detector from -61° to 68° by Dr. Ilke Arslan of Sandia National Laboratories, Livermore, California and Dr. John P. Bradley of Lawrence Livermore National Laboratory, Livermore, California; aligned, reconstructed and visualized using Gatan’s 3D Reconstruction and 3D Visualization software; the iso-surfaces highlight two different intensity levels in the reconstruction.		Image of phosphorus-containing macromolecular assemblies in the cell nuclei of Drosophila larvae; dual-axis EFTEM tilt series acquired with a Gatan Tridiem energy filter from -66° to 66° by Dr. Maria Aronova and Dr. Richard Leapman, National Institutes of Health, Bethesda, Maryland; for each axis phosphorus L-23 series (20eV slit, pre-edge and post-edge) were collected; a jump ratio series was calculated and the data were aligned and reconstructed using IMOD (University of Boulder, Colorado); finally, the reconstruction was rendered in the Gatan 3D Visualization software; the inset highlights a sub-volume extracted using the 3D Visualization ROI tool.

Product Requirements

¹ Supported Electron Microscopes include most recent JEOL, FEI, ZEISS TEM/STEM microscopes. Microscope must have computer controlled 4-axis stage control. Contact Gatan to confirm compatibility.
² Supported Energy Filters include all Gatan Imaging Filters, most JEOL and ZEISS in-column filters when equipped with a Gatan CCD camera. Contact Gatan to confirm compatibility.
³ Supported DigiScan Compatible Detectors include the Gatan 805 BF/DF STEM detector and the Gatan 806 HAADF detector and others. Contact Gatan to confirm compatibility
⁴ Recommended Graphics Cards include recent high-end display cards from NVIDIA and ATI. Contact Gatan to confirm compatibility.

For complete product and ordering information, see the complete 3D Tomography Brochure or contact your local Sales Office.