Sources

References courtesy of Phil Williams (School of Pharmaceutical Sciences, Univ. of Nottingham, UK) and Cristian Ionescu-Zanetti (Univ. of California Santa Cruz) culled from discussions on the DI SPM Digest.  Dr. Williams has written a summary of these problems and their solutions.  He also has established an expandable list of references associated with SPM tips, distortions and image processing. [ follow link to bibliography ]
 

Observations.

1. G. Reiss, H. Bruckl, J. Vancea, R Lecheleer and E. Hastreiter. J. Appl. Phys. 70 523 (1991)
2. F. Zenhausern, M. Adrian, R. Emch, M. Taborelli, M. Jobin, P. Descouts. Ultramicroscopy 42-44 1168 (1992)
3. C. Bustamante, J. Vasenka, C. L. Tang, W. Rees, M. Githold and R. Keller. Biochemistry 31 22 (1992)
4. C. A. Goss, C. J. Blumfield, E. A. Irene, R. W. Murray. Lanmguir 9 2986 (1993)
5. S. J. Eppell, F. R. Zypman, R. E. Marcant. Lanmguir 9 2281 (1993)
6. W.-L. Shaiu, D. D. Larson, J. Vasenka and E. Henderson. Nucleic Acids Res. 21 99 (1993)
7. P. Markiewicz, M. Pollanen, and M.C. Goh "Orientational Dependency of Atomic Force Microscopic Images Revealed by Alzheimer Paired Helical Filaments"  http://www.weizmann.ac.il/surflab/peter/phfpaper/index.html (last modified, June 24, 2001)

1. R. Chicon, M. Ortuno and J. Abellan. Surf Sci. 181 107 (1987)
2. Ph. Niedermann and O. Fischer. J. Microsc. 152 93 (1988)
3. G. Reiss, J. Vancea, H. Wittmann, J. Zweck and H. Hoffmann. J. Appl. Phys. 67 1156 (1990)
4. D. Keller. Surf. Sci. 253 353 (1991)
5. G. S. Pingali and R. Jain. Proc. IEEE Workshop Applied Computer Vision. 282 (1992)
6. D. J. Keller and F. S. Franke. Surf. Sci. 294 409 (1993)
7. N. Bonnet, S. Dongmo, P. Vautrot, and M. Troyon. "A mathematical morphology approach to image formation and image restoration in scanning tunneling and atomic force microscopies" Microsc. Microanal. Microstruct., 5, 477 (1994)
8. Drummond, C.J. and Senden, T.J. "The geometry of interaction in atomic force microscopy." Colloids and Surfaces 87, 217-234, (1994)

1. E. J. van Loenen, D. Dihkkamp, A. J. Hoeven, J. M. Lenssinck and J. Dieleman. Appl. Phys. Lett. 56 1755 (1990)
2. L. Montelius and J. O. Tegenfeldt. Appl. Phys. Lett. 62 2628 (1993)
3. J. Vasenka, S. Manne, R. Giberson, T. March and E. Henderson Biophys. J. 65 992 (1993)
4. J. Vasenka, R. Miller, E. Henderson. Rev. Sci. Instrum. 65 2249 (1994)
5. P. Markiewicz and M. C. Goh. Langmuir 10 5 (1994)
6. S. Xu and M. F. Arnsdorf J. Microsc. 183 199 (1994)
7. D. L. Wilson, K. S. Krump, S. J. Eppel and R. E. Marchant. Lanmguir 11 265 (1995)
8. T. O. Glaseby, G. N. Batts, M. C. Davies, D. E. Jackson, C. V. Nicholas, M. D. Purbrick, C. J. Roberts and P. M. Williams. Surf. Sci. Lett. 318 1219 (1994)
9. F. Atamny and A Bailer. Surf. Sci. 323 L314 (1995)

1. J. Villarrubia. "Morphological estimation of tip geometry for scanned probe microscope." Surf. Sci. 321 287 (1994)
2. J. Villarrubia. "Scanned probe microscope tip characterization without calibrated tip characterizers." J. Vac. Sci. Technol. B14 1518 (1996)
3. P. M. Williams, K. M. Shakesheff, M. C. Davies, D. E. Jackson, C. J. Roberts and S. J. B. Tendler. Langmuir 12 3468 (1996)
4. P. M. Williams, K. M. Shakesheff, M. C. Davies, D. E. Jackson, C. J. Robers and S. J. B. Tendler. "Blind reconstruction of scanning probe microscope image data" J. Vac. Sci. Technol. B14 1557 (1996)
5. P. M. Williams, K. M. Shakesheff, M. C. Davies, D. E. Jackson, C. J. Roberts, and S. J. B. Tendler, J. Vac. Sci. Technol., B 14, 1557 (1996)
6. J. Schneir, J. S. Villarrubia, T. H. McWaid, V. W. Tsia and R. Dixson. J. Vac. Sci. Technol. B14 1540 (1996)
7. S. Dongmo, M. Troyon, P. Vautrot, E. Delain and N. Bonnet. "Blind restoration method of scanning tunneling and atomic force microscopy images." J. Vac. Sci. Technol. B14 1552 (1996)
8. P. M. Williams, M. C. Davies, C. J. Roberts and S. J. B. Tendler. Appl. Phys. A66 S911 (1998)
9. S. Dongmo, J. S. Villarrubia, S.N. Jones, T.B. Renegar, M.T. Postek, and J.F. Song. "Tip characterization for scanning probe microscope width metrology" Submitted 3/16/98 to Characterization and Metrology for ULSI Technology, D. G. Seiler, W. M. Bullis, A. C. Diebold, R. McDonald, and T. Shaffner, eds., AIP Press, New York.

• J. S. Villarrubia, Algorithms for Scanned Probe Microscope Image Simulation, Surface Reconstruction, and Tip Estimation. J. Res. Natl. Inst. Stand. Technol. 102(4), 425 (1997).

This article by Villarrubia provides the actual source code.

• Peter Markiewicz, MIDAS98 Deconvolution Software.

Dr. Markiewicz's Web site is designed to explain and promote a dilation/erosion processor designed specifically for atomic force microscopy.   It also provides informaton about other software for deconvolution and image analysis and a bibliography.
 
• Other third-party software for SPM Image Analysis.

Eliminating tip effects.

"Eliminating tip effects is, well, tricky.  I would like to say impossible, but that would be the end to much of my research.  Distortion due to tip effects in SPM can be split into three:  geometric effects, point-spread effects, and interaction effects.

Geometric:  The first is the primary concern of most papers on the field. The distortion is due a function of how the probe profiles the surface; I.e. how it rides over the bumps and cracks.  To profile the surface accurately, one needs a nice sharp (often expensive) probe.  The interaction is non-linear; i.e. the convolution is not spatially invariant over the sample.  The best way to account for this geometric effect is to use the morphological erosion process (envelope reconstruction etc).  However, since the distortion is equivalent to a dilation, the reconstruction process does not add anything new to the data.  In general, those areas where the image is distorted correspond to those areas where the tip apex hasn't touched the sample.  So no amount of processing can reveal the topography of the sample at these points.  The value of doing this reconstruction is that one can find where the distortions have occurred.  This is very useful.  Papers by us (P. M. Williams), P. Markiewicz and M. Tegenfeldt highlight these ideas.

Point-Spread:  These effects are proper 'convolutions'  If you think of the field below an STM probe, the tunnel current flows through a finite area, albeit very thin and Gaussian in cross section.  These effects can be removed (the image deblurred) using normal deconvolution methods such as Maximum Likelihood, Weiner inverse filtering, and Jansson van Cittert.

Interaction effects:  These can be very large, or very small, and almost impossible to predict, measure, and account for.  Our Langmuir paper shows how difficult and significant these effects can be.  Using nice sharp probes to remove the geometric distortion increases the potential for sample interaction distortions. "

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Revised:  August 6, 2001
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