and Image Restoration
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 ]
G. Reiss, H. Bruckl, J. Vancea, R Lecheleer and E. Hastreiter. J. Appl.
Phys. 70 523 (1991)
F. Zenhausern, M. Adrian, R. Emch, M. Taborelli, M. Jobin, P. Descouts.
42-44 1168 (1992)
C. Bustamante, J. Vasenka, C. L. Tang, W. Rees, M. Githold and R. Keller.
31 22 (1992)
C. A. Goss, C. J. Blumfield, E. A. Irene, R. W. Murray. Lanmguir
9 2986 (1993)
S. J. Eppell, F. R. Zypman, R. E. Marcant. Lanmguir 9 2281 (1993)
W.-L. Shaiu, D. D. Larson, J. Vasenka and E. Henderson. Nucleic Acids
Res. 21 99 (1993)
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)
Tip self-imaging and
back-calculation of tip-shape
R. Chicon, M. Ortuno and J. Abellan. Surf Sci. 181 107 (1987)
Ph. Niedermann and O. Fischer. J. Microsc. 152 93 (1988)
G. Reiss, J. Vancea, H. Wittmann, J. Zweck and H. Hoffmann. J. Appl.
Phys. 67 1156 (1990)
D. Keller. Surf. Sci. 253 353 (1991)
G. S. Pingali and R. Jain. Proc. IEEE Workshop Applied Computer Vision.
D. J. Keller and F. S. Franke. Surf. Sci. 294 409 (1993)
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)
Drummond, C.J. and Senden, T.J. "The geometry of interaction in atomic
force microscopy." Colloids and Surfaces 87, 217-234, (1994)
methods based on morphology and trial-and-error.
E. J. van Loenen, D. Dihkkamp, A. J. Hoeven, J. M. Lenssinck and J. Dieleman.
Phys. Lett. 56 1755 (1990)
L. Montelius and J. O. Tegenfeldt. Appl. Phys. Lett. 62 2628 (1993)
J. Vasenka, S. Manne, R. Giberson, T. March and E. Henderson Biophys.
J. 65 992 (1993)
J. Vasenka, R. Miller, E. Henderson. Rev. Sci. Instrum. 65 2249
P. Markiewicz and M. C. Goh. Langmuir 10 5 (1994)
S. Xu and M. F. Arnsdorf J. Microsc. 183 199 (1994)
D. L. Wilson, K. S. Krump, S. J. Eppel and R. E. Marchant. Lanmguir
11 265 (1995)
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)
F. Atamny and A Bailer. Surf. Sci. 323 L314 (1995)
J. Villarrubia. "Morphological estimation of tip geometry for scanned probe
microscope." Surf. Sci. 321 287 (1994)
J. Villarrubia. "Scanned probe microscope tip characterization without
calibrated tip characterizers." J. Vac. Sci. Technol. B14 1518 (1996)
P. M. Williams, K. M. Shakesheff, M. C. Davies, D. E. Jackson, C. J. Roberts
and S. J. B. Tendler. Langmuir 12 3468 (1996)
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)
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)
J. Schneir, J. S. Villarrubia, T. H. McWaid, V. W. Tsia and R. Dixson.
Vac. Sci. Technol. B14 1540 (1996)
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)
P. M. Williams, M. C. Davies, C. J. Roberts and S. J. B. Tendler. Appl.
Phys. A66 S911 (1998)
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.
Peter Markiewicz, MIDAS98
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
Eliminating tip effects.
By Phil Williams (School of Pharmaceutical Sciences, Univ. of Nottingham,
"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
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
Copyright © John W. Cross