Processing and Quantifying Images

  • David B. Williams
  • C. Barry Carter


In this chapter we will equate processing with the use of the computer to analyze our data. We will simply use image processing to extract more information from the data than we can obtain by eye. The data will generally be an HRTEM image but could be other images or DPs. We’ll quantify spectra after we describe them in Part 4 of this text. In the past, the optical bench was also used for this purpose, but the number of optical benches is negligible compared to the number of computers now found in every TEM lab. Optical benches did allow us to form DPs which we could then modify to produce a processed image. This analog approach has now largely been replaced by its digital counterpart. The computer can be much cheaper than the optical bench and is far more flexible. The number of software packages which are designed for, or can easily be adapted to, TEM is also growing.


HRTEM Image Adaptive Filter Tilt Boundary Optical Bench Dark Ring 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Processing Images

  1. Harrel, B et al. 1995 Using Photoshop for Macintosh Que Indianapolis. A detailed description of the possibilities using Photoshop; this volume should also serve as a warning for all microscopists. Ask the question: has the image you are examining been processed, and if so, how?Google Scholar
  2. Hawkes, PW, Ed. 1980 Computer Processing of Electron Microscope Images, Springer-Verlag New York. Despite its age, this collection of articles is for advanced students.Google Scholar

Analyzing C s, Δf, ETC.

  1. Krivanek, OL 1976 Method for Determining the Coefficient of Spherical Aberration from a Single Electron Micrograph Optik 45, 97–101. An early paper giving a method for analyzing C s and Δf using a diffractogram.Google Scholar
  2. Zemlin, F, Weiss, K, Schiske, P, Kunath, W and Herrmann, K-H 1978 Come-Free Alignment of High Resolution Electron Microscopes with the Aid of Optical Diffractograms Ultramicrosc. 3 49. The Zemlin tableau paper.CrossRefGoogle Scholar

Focal Series and Tilt Series

  1. Kirkland, EJ, and Siegel, BM, Uyeda, N and Fujiyoshi, Y 1982 Nonlinear high resolution image processing of conventional transmission electron micrography: II. Experiment Ultramicrosc. 9, 65–74.CrossRefGoogle Scholar
  2. Kirkland, AI, Saxton, WO, Chau, K-L, Tsuno, K and Kawasaki, M 1995 Super-resolution by aperture synthesis: tilt series reconstruction in CTEM Ultramicrosc. 57, 355–374.CrossRefGoogle Scholar
  3. Kirkland, AI, Meyer, RR and Chang L-YS 2006 Local Measurement and Computational Refinement of Aberrations for HR TEM Microsc. Microanal. 12 461–468.CrossRefGoogle Scholar
  4. Kirkland, AI and Meyer, RR 2004. ‘Indirect’ High-Resolution Transmission Electron Microscopy: Aberration Measurement and Wavefunction Reconstruction Microsc. Microanal. 10 401–413.CrossRefGoogle Scholar

Advanced TEM Processing

  1. Dorset, DL 1995 Structural Electron Crystallography Plenum New York. An early example of 3D reconstruction.Google Scholar
  2. Downing, KH 1992 Scanning Microscopy Supplement 6 AMF O’Hare IL p. 405.Google Scholar
  3. Hawkes, PW, Ed. 1992 Signal and Image Processing in Microscopy and Microanalysis Scanning Microscopy Supplement 6, AMF O’Hare IL. This volume and its 1988 and 1996 companions are required reading for this subject.Google Scholar
  4. Hawkes, PW, Ottensmeyer, FP, Rosenfeld, A and Saxton, WO (Eds) 1988 Image and Signal Processing for Electron Microscopy Scanning Microscopy Supplement 2 AMF O’Hare IL.Google Scholar
  5. Hawkes, PW, Saxton, WO and Frank, J Eds. 1996 Image Processing Scanning Microscopy Supplement X AMF O’Hare IL.Google Scholar
  6. Russ, J.C. (1990) Computer-Assisted Microscopy Plenum Press New York. Chapter 3 is particularly relevant. Subsequent chapters give detailed analyses of the topics introduced here.Google Scholar
  7. Russ, JC 1995 The Image Processing Handbook 2nd edition CRC Press Boca Raton. A beautiful, comprehensive, and an essential component of any EM lab (or home).Google Scholar
  8. Saxton, WO 1992 Scanning Microscopy Supplement 6, AMF O’Hare IL p. 405. Correcting for distortion in the specimen (Section 31.6B).Google Scholar
  9. Trus, BL, Unser, M, Pun, T and Stevens, AC 1992 Scanning Microscopy Supplement 6, AMF O’Hare IL p. 441.Google Scholar

Chemistry From Images (Section 31.10)

  1. Kisielowski, C, Schwander, P, Baumann, FH, Seibt, M, Kim, Y, and Ourmazd, A 1995 An Approach to Quantitative High-Resolution Transmission Electron Microscopy of Crystalline Materials Ultramicrosc. 58, 131–155.CrossRefGoogle Scholar
  2. Ourmazd, A Baumann, FH, Bode, M and Kim, 1990 Quantitative Chemical Lattice Imaging: Theory and Practice Ultramicrosc. 34, 237–255.CrossRefGoogle Scholar

Pattern Recognition and Filtering on Interfaces

  1. King, WE and Campbell, GH 1993 Determination of Thickness and Defocus by Quantitative Comparison of Experimental and Simulated High-Resolution Images Ultramicrosc. 51, 128–135.CrossRefGoogle Scholar
  2. King, WE and Campbell, GH 1994 Quantitative HREM Using Non-Linear Least-Squares Methods Ultramicrosc. 56, 46–53.CrossRefGoogle Scholar
  3. Möbus, G, Necker, G and Rühle, M 1993 Adaptive Fourier-Filtering Technique for Quantitative Evaluation of High-Resolution Electron Micrographs of Interfaces Ultramicrosc. 49, 46–65. The adaptive Fourier-filtering technique.CrossRefGoogle Scholar
  4. Paciornik, S, Kilaas, R, Turner, J, and Dahmen, U 1995 A Pattern Recognition Technique for the Analysis of Grain Boundary Structure by HREM Ultramicrosc. 62, 15–27. Pattern recognition at interfaces.CrossRefGoogle Scholar


  1. Erickson, HP and Klug, A 1971 Measurement and Compensation of Defocusing and Aaberrations by Fourier Processing of Electron Micrographs Phil. Trans. Roy. Soc. London B. 261, 105–118. An example from the Nobel Prize winner.CrossRefGoogle Scholar
  2. Frank, J 1980 in Computer Processing of Electron Microscope Images, Springer-Verlag New York. p. 187. Correlation techniques (Section 31.12).Google Scholar
  3. Hÿtch, MJ and Stobbs, WM 1994 Quantitative Comparison of High Resolution TEM images with image simulations Ultramicrosc. 53 191–203. A very interesting conclusion on the thickness of the specimen.CrossRefGoogle Scholar
  4. Koster, AJ, van den Bos, A and van der Mast, KD 1988 Scanning Microscopy Supplement 2 AMF O’Hare IL p. 83. Autoalignment of the TEM.Google Scholar
  5. Koster, AJ and de Juijter, WJ 1992 Practical Autoalignment of Transmission Electron Microscopes Ultramicrosc. 40 89–107. Autoalignment of the TEM.CrossRefGoogle Scholar
  6. Krivanek, OL and Mooney, PE 1993 Applications of Slow-Scan CCD Cameras in Transmission Electron Microscopy Ultramicrosc. 49 95–108. Autoalignment of the TEM.CrossRefGoogle Scholar
  7. Moré, JJ 1977, in Lectures Notes in Mathematics, Ed. G.A. Watson p. 630 Springer Berlin.Google Scholar
  8. Moré, JJ, Garbow, BS and Hillstrom, KE 1980 User Guide for MINIPACK-1.Google Scholar
  9. Saxton, WO and Koch, TL 1982 Interactive Image Processing with an Off-Line Minicomputer: Organization, Performance and Applications J. Microsc. 127 69–83. Autoalignment of the TEM.Google Scholar
  10. Saxton, WO, Smith, DJ and Erasmus, SJ 1983 Procedures for Focusing, Stigmating and Alignment in High Resolution Electron Microscopy J. Microsc. 130 187–201. Cross-correlating pairs of images.Google Scholar
  11. Tang, D, Jansen, J, Zandbergen, HW and Schenk, H 1995 The Estimation of Crystal Thickness and the Restoration of Structure-Factor Modulus from Electron Diffraction: A Kinematical Approach Acta Cryst. A51 188–197. (31.6E) Quantitative analysis of DPs.Google Scholar
  12. van Heel, M, Winkler, H, Orlora, E and Schatz, M 1992 Scanning Microscopy Supplement 6, AMF O’Hare IL p. 23. Review of TEM of beam-sensitive materials.Google Scholar
  13. Zou, XD 1995 Electron Crystallography of Inorganic Structures, Chemical Communications Stockholm University, Stockholm, Sweden.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.The University of Alabama in HuntsvilleHuntsvilleUSA
  2. 2.University of ConnecticutStorrsUSA

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