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Application of 3 x 3 Transformation Matrix in the Correction of Three-

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SCANNING VOL. 33, 94–98 (2011)
& Wiley Periodicals, Inc.
Application of 3  3 Transformation Matrix in the Correction
of Three-Dimensional AFM Image Tilts Through Coordinate
Transformation
ADEDAYO S. ADEBAYO, XUE-ZENG ZHAO, FEI WANG,
Department of Mechatronics Engineering, Harbin Institute of Technology, Harbin, China
Summary: In atomic force microscopy (AFM), it is
difficult to maintain samples in a perfect horizontal
position on the piezoelectric stage of an AFM to
obtain accurate measurement of surface features
and to enhance the visual effect of topographic
images. Correction of the tilted image therefore
requires the use of an appropriate 3  3 transfor-
mation matrix which will transform the coordinates
to simultaneously correct the tilt in both the x-and
y-axes due to the three-dimensional nature of AFM
images. In this study, application of transformation
matrix in three-dimensions for the simultaneous
correction of image tilts in both the x- and y-axes by
the method of coordinate transformation in three-
dimensions is presented. Application of the matrix
in simultaneously correcting tilts in the x- and
y-axes of an AFM image is implemented by simu-
lating an image assuming there are tilts in both the
x- and y-axes. Results of features measurement after
transforming the coordinates with the matrix show
the efficacy of the matrix. This will conveniently
replace the line-by-line analysis done to remove tilts
in AFM, which has been the practice long before
now. It also has the advantage of correcting images
by simultaneously removing tilts in both the x- and
y-axes as a veritable replacement of having to
separately correcting tilts in images. This matrix can
be used to transform coordinates in three-dimen-
sions to obtain accurate step height and linewidth in
Contract grant sponsor: National Natural Science Foundation of
China; Contract grant number: 10902031.
Address for reprints: Zhao Xue-zeng, P. O. Box No. 306, Harbin
Institute of Technology, 92 Xi-Dazhi Street, Nangang District,
Harbin 150001, China
E-mail: zhaoxz@hit.edu.cn
Received 10 December 2010; Accepted with revision 9 February
2011
DOI 10.1002/sca.20227
Published online 31 March 2011 in Wiley Online Library (wiley
onlinelibrary.com)
AND FAQUAN ZHOU
AFM images. SCANNING 33: 94–98, 2011.
r 2011 Wiley Periodicals, Inc.
Key words: orthogonality, transformation matrix,
image tilt, AFM, coordinate transformation
Introduction
In atomic force microscopy (AFM), it is difficult to
maintain samples in a perfect horizontal position on
the piezoelectric stage of an AFM. AFM is an in-
strument used to image surface topography (Liu et al.,
2005) and measure features in three-dimensions at the
nano-scale. Image correction or tilt removal is done on
AFM images as a result of the difficulty in perfectly
maintaining samples in horizontal position. This sample
tilt results in poor visual effect of topographic
images and leads to inaccurate results of measurand
such as step height and linewidth. Tilts occur both in
the fast-scan (x-) and the low-scan (y-) axes. Im-
perfection in sample manufacture also accounts for
this tilt in the image (Fu et al., 2008). Correction of
the tilted image requires the application of a transforma-
tion matrix to be used in the coordinate transfor-
mation method which will transform the coordinates in
three-dimensions while simultaneously correcting the
image tilts in both the x- and y- axes. This will save a lot
of time in processing an AFM image which before now
has been done by either separately removing tilts in the
x-axis and then the y-axis or by carrying out a line-by-
line analysis of the image to determine the line of best fit.
Remarkable progress has been made in the method of
analysis in two-dimensions to correct the tilt in the x-axis
(Fu et al., 2008) when there is tilt along the x-axis only,
assuming no tilt in the y-axis which is important in the
determination of features dimension of samples. Equal
attempt of fundamental importance has also been made
at image correction by separately carrying out analysis in

the x- and y-axes (Misumi et al., 2006), this however is
time consuming. AFM images are in three-dimensions
(Dixson et al., 2000; Mininni et al., 2007), as most
engineering and physical problems. On the macro- and
micro-scale, three-dimensional problems are often
idealized to two-dimensions to simplify the analysis
involved. Such idealization or simplification has been
known to give reasonable solution to practical problems
of engineering interest but often leads to loss of
vital information or data along the lateral direction of
AFM images on the nano-scale. In Solid Mechanics,
we talk of plane stress problems where for example a
thin disc is uniformly loaded along its periphery while
taking the disc dimensions along the z-axis as
infinitesimally small; and a plane strain problem
where an infinitely long circular cylinder is subjected to
uniform loading internally or externally such that the
change in length is negligibly small (Timoshenko and
Goodier, ’51). In Fluid Mechanics also, approximation
to two-dimensional analysis for axial-flow turbines
and compressors assumes flow is invariant in the
circumferential direction and that no radial velocities
occur (Dixon, ’95). These simplifications are valid as far
as measurements and analysis go at the macro- and
micro-scale whose validity may be questioned at the
nano-scale.
Current method of image processing to remove
arbitrary tilts in AFM images has been by finding
the best fit through line-by-line analysis of the sub-
strate profile and subtracting this background from
all data points (Fu et al., 2008). Misumi et al. (2006)
also worked on removing tilts in AFM images by
separately treating x-axis and then y-axis.
In this study, we demonstrate the application of a
3  3 transformation matrix in the successful correction
of arbitrary tilts in AFM images using the coordinate
transformation method in three-dimensions. This will
be done in one operation as opposed to the method of
separately correcting tilts in x- and then y-axis (Misumi
et al., 2006). We simulated an AFM image with tilts in
both the x- and y-axes with different angles of tilt and
presented the result. The trend in the result shows that
the 3  3 transformation matrix is efficient compared
with the previous technique of correcting tilts sepa-
rately in the x- and y-axes as tilts in both the x- and
y-axes could be removed simultaneously thereby saving
time and eliminating errors associated with the presence
of arbitrary tilts in an AFM image. This makes the
transformation matrix suitable for use in the three-
dimensional coordinate transformation method of tilt
removal or image correction in AFM images.
Theoretical Framework
Image tilts need to be corrected for accurate
measurement of surface features such as step height
A. S. Adebayo et al.: 3D transformation matrix 95
and linewidth; this also enhances the visual effect of
the profile image. This image tilts are caused by
misalignment in the measuring frame and the
sample frame in an AFM due to improper image
processing, difficulty in maintaining a perfect hori-
zontal position for the sample on the PZT stage,
topographic imperfections of samples, local defects
in samples, waviness of the surface on a global scale
(Fu et al., ’99). To simultaneously correct these tilts
in AFM images both in the x- and y-axes and to
eliminate the error due to the misalignment in both
the measuring and sample frames, coordinate
transformation in three-dimensions is proposed.
The choice of coordinate transformation in three-
dimensions is however hinged on the application of
a valid 3  3 orthogonal transformation matrix in
multiplying the sample coordinates to align them
with the measuring coordinate axes for an error-free
features measurement. This matrix must be ortho-
gonal for it to be suitable for the image correction in
both the x- and y-axes at the same time.
 We simulated a single-step AFM image of a
profile with the specimen assumed to be tilted in
both the x- and y-axes, we then applied the 3  3
transformation matrix in correcting these tilts
simultaneously and the results of the features
measured (H, W, AR and AL) presented.
 To further test the stability of the result, the angle
of tilt is then varied in steps of 0.5o along the
y-axis and the result presented. Comparing the
results show a promising trend which agrees with
the published results in a two-dimensional case.
Method and Implementation Procedure
There are three fundamental rigid transforma-
tions (Milewski, ’94): translation, rotation, and
reflection. Here we shall be considering only rotation,
as we are taking our rotation about the origin, i.e.
the measuring and sample frames have a common
centre.
In three-dimensions unlike in two-dimensions,
objects and shapes are represented in x, y, and z
directions. Representation of objects in 3D gives a
measure of the volume of such objects. For a 3D
case, the rotation (transformation) matrix R is given
as (Ginsberg, 2008)
2 3
cos y cos f sin y cos f  sin f
R ¼ 4  sin y cos y 0 5 ð1Þ
cos y sin f sin y sin f cos f
This is in agreement with the Cartesian co-
ordinates in three-dimensions as in Figure 1.
In AFM, the arrangement of the coordinate
axes is as shown in Figure 2. Two operations are
96 SCANNING VOL. 33, 2 (2011)

Fig 1. The rectangular coordinates system in three-dimen-

sions. P(x,y,z) is a point in the three-dimensional space. OX,
OY and OZ are three coordinate axes perpendicular to each
other and arranged in a right-handed manner. Turning form
OX to OY in a positive direction of OZ gives a right-handed
screw motion. Fig 3. P and Q are points in the x,y,z space with coordinates
P(x1,y1,z1) and Q(x2,y2,z2), which become P0 and Q0 in the
x0 ,y
0
0 0
,z
0
space after transformation. Length |PQ| is equal to
|P Q |after rotation.

i.e.
2 03 2 3
x sin y cos f cos y cos f  sin f
6 07 6 7
4 y 5 ¼ 4 sin y sin f cos y sin f cos f 5
Fig 2. The three-dimensional coordinates system of an
AFM. X is the fast-scan axis whereas Y is the slow-scan z0 cos y  sin y 0
(lateral) axis.

performed on the rotation matrix in equation 1 to  ½x y z 0 ð4Þ

give matrix A (Equation (2)) in line with the Therefore Equation (4) is the true transformation
arrangement of coordinates to ensure its suitability equation for a three-dimensional case of the image
in transforming AFM images in three-dimensions. of a sample obtained by an AFM. This can be used
The first is interchanging column 1 and column 2 to correct the AFM image tilts in three dimensions
and also row 3 and row 2. These of course preserve where there are tilts in both the x- and y-axes
the orthogonality requirements of the transforma- simultaneously.
tion matrix as the determinant remains unchanged
after the row and column interchange
2 3
sin y cos f cos y cos f  sin f Simulation and Results
A ¼ 4 sin y sin f cos y sin f cos f 5 ð2Þ
cos y  sin y 0 To test the applicability of the 3  3 transforma-
tion matrix, we simulated an AFM image of a single
So for a three-dimensional case, P(x,y,z) is an
step profile (Fig. 4) with MATLAB (version 7.8) by
imaginary point in space containing the data set
tilting the sample by 21 along the x-axis while
of an AFM image. By premultiplying the point
varying the angle of tilt between 1.51 and 2.51 in
P(x,y,z) in Figure 1 with the transformation matrix
steps of 0.51 along the y-axis using the following
A, P is transformed to P0 (x0 ,y0 ,z0 ). All data points in
parameters: 400 nm top width (W), 600 nm step
the image domain are transformed by the following
height (H), the left (AL) and right (AR) sidewall
transformation equation as in Figure 3
angles were taken to be 851 while the range of the
2 03
x image was 128  128 pixels with a resolution of
6 07 0 5 nm.
4 y 5 ¼ ½A  ½x y z ð3Þ
0
As in Equation (4) above, each data point in
z the image domain is transformed according to
 A. S. Adebayo et al.: 3D transformation matrix 97

Fig 4. (A) The simulated image and (B) its line profile. H is the step height, W is the top width, AR and AL are the right and left
sidewall angles, y and f are the respective angle of tilts along the x- and y-axes.

Equation (5) below: TABLE I Calculated results of features of the simulated single
2 03 2 3 step profile with y 5 21 and f 5 1.51 as the respective angle of
x sin y cos f cos y cos f  sin f tilts in the x- and y-axes
6 07 4
4 y 5 ¼ sin y sin f cos y sin f cos f 5
Coordinate
z0 cos y  sin y 0 Result obtained transformation
2 3 from previous using the new
x Features Initial data work matrix
6 7
4 y5 ð5Þ W (nm) 400 399.612 399.141
z H (nm) 600 600.366 599.4195
AL 851 85.3871 84.1411
After transformation, each ordered pair of co- AR 851 85.4171 84.716
ordinates (x,y,z) now becomes (x0 ,y0 ,z0 ), as in
W and H are top width and step height, respectively, whereas
Equation (6). Calculation of features dimension (H,
AR and AL are the right and left sidewall angles.
W, AL, AR) can then be carried out. Details of
features calculation procedures are published in
Zhao et al. (2003). TABLE II Calculated results of features of the simulated single
step profile with y 5 21and f 5 21 as the respective angle of
x0 ¼x sin y cos f1y cos y cos f  z sin f tilts in the x- and y-axes
y0 ¼x sin y sin f1y cos y sin f1z cos f ð6Þ
Coordinate
z0 ¼x cos y  y sin y Result obtained transformation
from previous using the
After transforming the coordinates with the 3  3 Features Initial data work new matrix
transformation matrix, the result is as shown in
W (nm) 400 399.612 399.147
Tables I–III. The top width W of 400 nm dimension H (nm) 600 600.366 599.257
was shorten to 399.612 and 399.141 nm by using the AL 851 85.3871 84.0781
method developed by Fu et al. (2008) and our new AR 851 85.4171 84.3931
transformation matrix, respectively, the step height
W and H are top width and step height, respectively, whereas
H was reduced to 599.4195 nm by using the new AR and AL are the right and left sidewall angles.
matrix as different from the 600.366 nm obtained
with the earlier method of Fu et al.’s (2008).
AL and AR were calculated to be 84.141 and 84.7161 TABLE III Calculated results of features of the simulated single
step profile with y 5 21and f 5 2.51 as the respective angle of
as against 85.387 and 85.4171 using the method tilts in the x- and y-axes
of Fu et al. ’s (2008) when y 5 21 and f 5 151
(see Table I). Tables II and III show the results of Coordinate
the measured features when f 5 2 and 2.51. Result obtained transformation
from previous using the
Features Initial data work new matrix
Discussion W (nm) 400 399.612 399.147
H (nm) 600 600.366 599.048
Any orthogonal transformation in the plane or AL 851 85.3871 83.8551
AR 851 85.4171 84.2231
three-dimensional space is a rotation (Kreyszig,
2006). Premultiplication of a linear transformation W and H are top width and step height, respectively, whereas
by an orthogonal matrix corresponds to pure AR and AL are the right and left sidewall angles.
 98 SCANNING VOL. 33, 2 (2011)
rotation that preserves the length between any two
points in space and also angles between any two
straight lines (Jeffrey, 2002). The previous idealiza-
tion which assumes the sample is tilted through an
angle y along the x-axis only limits the information
available for the accurate determination of features
such as step height and linewidth along the y-axis.
We applied this orthogonal matrix for the
coordinate transformation of the sample coordinate
axes to the measuring axes based on the previous
inspiring work by Fu et al. (2008). The 3  3 matrix
is useful in image correction by coordinate trans-
formation when there is image tilt through angles y
and f along the x- and y-axes, respectively, as
shown in Figure 4. The trend of features in the
results is in perfect agreement with that of Fu et al.
(2008), though with different initial data as shown in
Tables I–III. The second column of Tables I–III is
the initial data of the simulated sample, the third
column is the measured data using the earlier deri-
vation in 2-D by Fu et al. (2008) assuming there is
tilt only in the x-axis while the last column shows
the result with the coordinate transformation in
three-dimensions using the 3  3 transformation
matrix.
Conclusion
Implementation of a 3  3 transformation matrix
for accurate determination of surface features
dimension of AFM images on the nano-scale using
the coordinate transformation method was pre-
sented in this study. The transformation matrix was
tested by simulating a single-step profile of an AFM
image with tilts in the x-and y-axes, features such as
step height (H), top width (W), and the right (AR)
and left (AL) sidewall angles were measured and the
result confirmed the accuracy of the transformation
matrix. Further work would have to be on subjecting
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the transformation matrix to rigorous test under
experimental conditions with very small feature
dimensions to ascertain the stability of the results of
features measurement particularly at the 45 nm
technology node and beyond.
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