Image Analysis Facility
The NCEM image analysis facility supports NCEM users’ computational needs. The facility offers an array of computers running a number of commercial scientific software packages for image processing, image simulation, and quantitative data analysis, to obtain structural information from images taken on NCEM's electron microscopes. Software image processing and analysis facilities are available at several user stations in the computer user area. (Instrument schedule and requirements: 24 hours daily; no restrictions for approved users.)
For more information contact: John Turner.Software
Image processing and analysis facilities are available at several user stations in the computer user area. Listed below are the main software packages applied in the area of image simulation, image processing and modelling. In addition, there are software packages for data analysis, plotting, image visualization and general presentation.
Image Simulation / Crystallography
- MacTempas is a general HRTEM image simulation software package running on NCEM’s Apple Macintosh computers. An add-on package for quantitative comparison of images and automatic parameter and structure refinement is currently being developed at NCEM.
- Desktop Microscopist is available on four Macintosh workstations and provides a number of useful functions, ranging from tables of d-spacings and angles to CBED patterns, Kikuchi maps and search of the Electron Diffraction Database for identification of unknown compounds.
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Through-focus series of ARM images of [001] mullite, showing the presence of an oxygen-deficient column, is confirmed by image simulations. More at: T. Epicier, M.A. O'Keefe and G.Thomas, Acta Cryst. A46 (1990) 948-962. |
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Simulated HRTEM images of a cubeoctahedron consisting of 561 Pd atoms, representing a typical catalyst particle. In experimental HRTEM investigations of dispersed catalysts, the orientations of the nanoparticles with respect to the incident electron beam are unknown. A large proportion of the particles present in any micrograph field will show the presence of lattice fringes, leading to a first impression that many particles must lie close to zone-axis orientations. Since these particles are sufficiently small to possess large reciprocal-space shape functions that will be intersected by the Ewald sphere for quite large tilts away from the nearest zone axis, the electron scattering produced by these intersections will often lead to lattice fringes that are not simply related to the crystal structure of the particles. Such misleading lattice fringes can lead to misidentification of the particles. |
Image Processing / Data Analysis
- Digital Micrograph is a general image processing package with many features specific to electron microscopy. DM has been extended by several plug-in programs that have been developed at NCEM.
- EmiSpec for off-line analysis of spectral information obtained at NCEM's analytical microscopes.
- "NCEMPackage" is an extension to Digital Micrograph and contains a number of routines for image processing, analysis and feature extraction. It includes peak finding, lattice refinement, displacement analysis, noise reduction filters, template matching, routines for use in holography, and more. It comes with an integrated help system covering the available commands.
- "Phase" is an extension to Digital Micrograph which uses the concept of the geometric phase to analyze variations in reciprocal space to quantitatively determine real space displacements, local lattice parameters and local strain. As with "NCEMPackage", an on-line help function is available.
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Example of structure determination by image processing and simulation. Original image (left) is windowed in Fourier space and embedded into simulated image of Y2Si2O7 (right). |
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Quantitative determination of local lattice parameter and composition across a quantum well through the use of the "Geometric Phase" software extension, which is a public domain software package available from NCEM. |
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Image processing and feature extraction using the NCEMPackage software extension to Digital Micrograph. The original image is that of Zeolite, which is rapidly being damaged under the electron beam. The final result shows the average image of the zeolite unit cell in the 010 direction. |
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Digitized high-resolution image of quasiperiodic asymmetrical 90° <110> tilt grain boundary in Al and cross correlation with a structural unit (inset) characteristic for this boundary. The location of these units in the boundary is indicated by white cross-correlation peaks. |
Atomic Modelling
- CrystalKit produces models of interfaces and defects for input to MacTempas.
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Example of modelling and image simulation of an interface between CoSi and Si. The model on the top was created in CrystalKit starting with two perfect lattices of CoSi and Si, defining the orientation relationship between the crystals, the interface plane and the zone axis. The model is shown slightly titled off the zone axis with the atomic bonds drawn. The atomic coordinates were then imported directly into MacTempas for simulation of the HRTEM image shown below [WHERE?]. |
Hardware
Presently the IAF equipment consists of the following:
- Four Apple Macintosh G4 workstations for image simulation, image processing and general computing are networked to a file server. One machine is connected to a LeafScan 16-bit scanner for input of images from negatives.
- One 200MHZ PC runs off-line data analysis and image processing.
- Two PCs are available for focal series reconstruction.
Input and Output
Since all the computers are networked together, data that is input using any particular input device can be made available on all computers; similarly, data on any computer can be sent to any output device. Users should bring sufficient storage media if network transfer is not available.
Input Media
- Negatives. Selected areas of experimental micrographs can be input as digitized images using a Flextight transmission scanner. This scanner supports a variety of negative sizes. For a 35mm film window, maximum resolution gives 5080 pixels by 7400 pixels. Images can be digitized at 8 or, for wider dynamic range, at 16 bits. This scanner accepts positive or negative transparencies in color or black/white.
- Prints. Can be scanned in as 8-bit pixels at a resolution of up to 3200 dots per inch through a Microtek scanner.
- Video tape and live video. Frames can be digitized (grabbed) as 8-bit images with 640 by 480 pixels.
Output Media
- Paper. Images can be output as laser printer halftones on 8.5" x 11" paper or on an Epson inkjet printer.
- Networks. User data (including simulated or processed images) can be output over ethernet to the user's own computer using FTP.