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Image denoising techniques applied to glow

discharge optical emission spectroscopy elemental
Cite this: J. Anal. At. Spectrom., 2014,
29, 315 mapping†
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Gerardo Gamez,*a Gaurav Mohantyb and Johann Michlerb

Received 24th September 2013
Accepted 13th November 2013
DOI: 10.1039/c3ja50312g
www.rsc.org/jaas
Glow discharge optical emission spectroscopy (GDOES) is becoming a mature technique for depth profiling
analysis. The advantages it affords, including fast, quantitative, and multi-elemental analysis, as well as
allowing very high depth-resolution, have attracted the attention of the thin film community. Recently,
the use of GDOES under pulsed-mode operation and coupled to hyper-spectral imaging techniques has
been proposed to perform surface elemental mapping. Several manuscripts have reported on the
underlying mechanisms in GDOES pertaining to the spatial resolution, while other manuscripts have
reported on elemental mapping applications, for example, regarding separated proteins or thin film
combinatorial libraries. Only a couple of studies have reported image processing techniques applied to
GDOES elemental mapping and none having to do with image denoising purposes. Herein, image
denoising techniques are compared in several scenarios: (a) mapping of homogeneous samples; (b)
mapping of heterogeneous samples in two dimensions; (c) mapping of heterogeneous samples in three
dimensions. Denoising techniques compared include averaging, median filtering, principal component
analysis (PCA), and local pixel grouping-PCA. The peak signal-to-noise ratio is used to show the
efficiency of noise removal, while the full-with-half-maximum of emission from sharp features is used to
demonstrate the resolution degradation effects of each denoising technique. In general, it is observed
that PCA outperforms other techniques albeit with a higher cost of image processing time. Also, it
becomes evident that having multiple image slices (a 3rd dimension) affords more efficient noise removal
while minimizing losses in spatial resolution.

et al.,10 which is several orders of magnitude faster than other

Introduction
GDOES is becoming a mature technique for depth proling
analysis.1–6 The advantages it affords include fast, quantitative,
and multi-elemental analysis with minimal-to-no sample prep-
aration. Also, GDOES allows very high depth-resolution (several
nm), thus this technique has attracted the attention of the thin
lm community.
Recently, the use of GDOES under pulsed-mode operation
and coupled to spectral imaging techniques has been proposed
to perform surface elemental mapping.7–12 This approach
becomes interesting once it is realized that elemental maps of
very large sample surfaces (e.g. 100 cm2) could be obtained in a
few tens of seconds, as proposed by Voronov et al.12 and Gamez
a
Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
79409, USA. E-mail: gerardo.gamez@ttu.edu; Fax: +1 806 7421289; Tel: +1 806
7423086
b
Swiss Federal Laboratories for Materials Science and Technology, Laboratory for
Mechanics of Materials and Nanostructures, Feuerwerkerstrasse 39, 3602 Thun,
Switzerland
† Electronic supplementary information (ESI) available. See DOI:
10.1039/c3ja50312g
techniques. Several manuscripts have reported on the under-
lying mechanisms in GDOES pertaining to the spatial resolu-
tion. Webb et al. showed that direct current pulsed-GDOES
affords sufficient lateral resolution to perform elemental
mapping.11 In addition, Gamez et al. showed that this is also the
case for radio frequency pulsed-GDOES.7 In both studies, the
effect of the operating conditions pertaining to pressure and
pulsing led the authors to conclude that the lateral resolution in
GDOES is limited by the residence time of the sputtered atoms
in the GD lamp as well as their mean free path. Other manu-
scripts have reported on elemental mapping applications.
Gamez et al. reported on the application of RF pulsed-GDOES
for elemental mapping of proteins blotted onto membranes.7
In addition, Gamez et al. showed the advantages, including
orders of magnitude faster analysis times, of using dc pulsed-
GDOES for measuring the elemental landscape of thin lm
composition spreads used in combinatorial libraries and high
throughput screening samples.10 Only a couple of studies have
reported image processing techniques applied to GDOES
elemental mapping. Engelhard et al. reported on the use of an
algorithm to correct for the geometric distortion on the images
collected with a Czerny–Turner monochromatic imaging

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spectrometer.13 Gamez et al. used an algorithm to correct for the
smile distortion on the images collected with a spectrograph at
the heart of a push-broom imaging system.8 To the authors’
knowledge, there are no studies investigating the effects of
image denoising techniques for GDOES elemental mapping.
Herein, image denoising techniques are compared in several
scenarios: (a) mapping of homogeneous samples; (b) mapping
of heterogeneous samples in two dimensions; (c) mapping of
heterogeneous samples in three dimensions. Denoising tech-
niques compared include mean ltering, median ltering, PCA,
and local pixel grouping (LPG)-PCA. The purpose is to identify
which technique provides better noise removal while preventing
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image blurring or maintaining the spatial resolution. The peak
signal-to-noise ratio (PSNR) is used to show the efficiency of
noise removal, while the full-width-half-maximum (FWHM) of
emission from sharp features is used to demonstrate the blur-
ring effects of the denoising techniques.
Experimental and methods
GDOES elemental mapping system
The GDOES elemental mapping system has been previously
described.8 In short, a push-broom hyper-spectral imaging
system is used to collect temporally, spectrally, and spatially
resolved images from a glow discharge lamp. The GD lamp is an
end-on Grimm-type geometry with an inner diameter of 7 mm.
The spectrograph’s (microHR manual, Jobin Yvon Horiba,
France) grating size was reduced from 32 mm
32 mm to 8 mm

8 mm with a mask to minimize aberrations and improve
spectral and spatial resolution. The spectral window acquired
by the ICCD (PI-Max 3 1024i, Princeton Instruments, USA) was
approximately 68.5 nm. Part of the system optics are mounted
on a motorized stage such that the collected image can be
scanned through the entrance slit without having to move the
spectrograph or the GD source. An in-house developed Lab-
VIEW program (National Instruments Corporation, Austin, TX,
USA) was used for the acquisition automation, and display of
hyper-spectral cube images.
The measurements were performed under the following
operating conditions: direct current pulsed-power mode, 2.5ms
GD pulse duration, 1 kHz GD pulse frequency, 23 Torr Argon
(99.9999% purity), 500 V GD pulse voltage (measured at
sample), 2
2 ICCD binning, 25  C ICCD temperature, ICCD
gain value of 80, 2 ms ICCD gate duration, start of ICCD gate
synchronized with start of GD pulse, 100 on-camera gate accu-
mulations per ICCD frame, 0.191 mm s1 motor stage speed, 8
mm motor stage scan distance. The time required to obtain a
single image (42 s) corresponds to a pixel size of 10 nm in
depth for a Cu substrate. It is important to note that the
acquisition conditions (CCD gain, gate width, accumulations)
of the imaging system will have an impact on the signal-to-noise
(SNR) ratio observed. It is always best to use conditions that
maximize SNR within the experimental limitations. The image
acquisition conditions implemented here were chosen to allow
the best spatial resolution, including the depth dimension,
under the dynamic range restrictions. Thus, these conditions
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could be used without having a previous knowledge of sample
homogeneity.
Samples
Several samples were used to obtain GDOES elemental mapping
images with different characteristics. The rst sample consisted
of a homogeneously deposited Ag thin lm on a Cu substrate
(99.9% Cu). The Ag lm was deposited by sputter coating (Balzers
Sputter Coater SCD 050) from an Ag target (99.99% Ag) under Ar
gas. The thickness of the lm was not determined but it was
enough to prevent sputtering through to the Cu substrate during
the measurements (at least 100 collected GDOES images) which
would correspond to several 100 s nm. The Ag emission at
338.3 nm was measured in this sample. The second sample
consisted of the same thin lm but perforated with the tip of a
needle such that the Cu substrate was accessible. The Cu emis-
sion at 324.7 nm was measured in this part of the sample and was
used for determination of the FWHM of the emission prole. The
third sample consisted of a Cu lm deposited by sputter coating
(Cu target 99.99% Cu) on a Ni substrate (99.9% Ni). A slant was
engineered into the Cu lm thickness, i.e. the thickness was not
homogeneous. The overall lm thickness (10–100 nm) was thin
enough to sputter through the Cu lm during the GDOES
elemental mapping experiment and a small perforation was
added to incorporate a lateral heterogeneity feature. The Ni
emission at 341.5 nm was measured on this sample.
Image processing
Different types of image processing techniques were applied to
the data. Part of the image processing was performed in MAT-
LAB (The MathWorks, Inc.) and another part, including the
display of 3D images, was performed with ImageJ (National
Institutes of Health, USA). Single image median ltering, or
median ltering in two dimensions, was performed using the
MATLAB function “medlt2”. Median ltering in three dimen-
sions was performed by arranging the images of interest into a
stack of images and using the 3D median lter tool in ImageJ.
The local pixel grouping PCA was performed following the
protocol from Zhang et al. and using their published MATLAB
code. The only alterations to the code consisted of bypassing the
PSNR section.
In addition to the measured depth prole images, a set of
model depth prole images was created. For this purpose, the
average of 100 images of the Ag 338.3 nm emission of the
homogeneous sample was used to serve as the mean of a
Gaussian distribution in depth. The MATLAB function
“normpdf” was used to create the distribution values. Further-
more, Gaussian noise was added to the images with the MAT-
LAB function “imnoise” such that the resulting noise
component was comparable to the one found in measured
images.
Full-width half maximum information was obtained by
tting a Lorentzian curve to the laterally resolved emission
proles. On the other hand, the depth-resolved emission
proles were tted to a Gaussian curve to obtain the FWHM in
depth.
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Results and discussion
Noise sources in GDOES have been studied before by looking at
the noise power spectrum (NPS) and have been shown to be
system specic. Broekaert et al. showed an NPS with white noise
and some peaks attributed to pump and line sources while
other peaks were unidentied.14 On the other hand, Winchester
et al. showed only white noise and dri in the NPS of their
GDOES source.15 Here, the rotationally averaged power spectra
(PS) of homogeneous sample images were determined (see ESI,
Fig. 1S†) to detect the possible contribution from different types
of noise. In short, the PS is the square of the Fourier transform
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of the images but in this case it is rotationally averaged to show
the more familiar magnitude vs. frequency plot. The PS of all
images show a 1/fn dependency at lower frequencies. This is due
to the contribution of the signal which is convoluted with the
noise. The PS for the single image of Ag sample levels off at
higher frequencies as opposed to the PS obtained from aver-
aging 100 single images. This comes from the contribution of
white noise which would give a at line in the PS if it was the
only contribution. It is instructive to show how certain things
can affect the PS. For example, the PS of an image of the
emission of a Ni sample previously taken using our system with
a faulty gas bottle regulator shows a peak at a spatial frequency
of 10. This comes from the intensity modulation in the corre-
sponding image that arises from pressure changes in the GD
lamp due to the faulty regulator. The images in this study do not
have such features and the only clearly distinguishable noise
has a white character.
The purpose of comparing the image denoising techniques
is to identify the most efficient denoising procedure for three
different cases: (a) images from samples with homogeneous
content, (b) images from samples with lateral heterogeneity,
and (b) images from samples with lateral and depth
heterogeneity.
(a) Images from samples with homogeneous content
The rst case (a) pertains to the denoising of images such as
those coming from standard reference materials. Such images
would be used for calibration purposes in quantitative GDOES
elemental mapping.10 The noise content would affect the stan-
dard deviation around the regression and image denoising
techniques would potentially improve quantitative results. The
PSNR parameter is used in this study to measure how effective is
the noise reduction. PSNR is typically used in image compres-
sion schemes to measure the quality of image reconstruc-
tion.16,17 It compares the maximum possible signal power
against the power of the noise and it is expressed in decibels to
accommodate large dynamic ranges:


MAXI 2
PSNR ¼ 10 log10
MSE
1X
m1 Xn1
 2
MSE ¼ Iði; jÞ  Kði; jÞ
mn i¼0 j¼0
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where, in our case, the maximum possible value of the image
(MAXI) is 65 536 for a 16 bit image. The MSE is the mean square
error when comparing an original image I of m
n pixels to a
noisy representation image K. Higher PSNR generally indicates
better quality. In our case, the “original image” or better said
the reference image, was obtained by averaging 100 GDOES
emission maps, at 338.3 nm, of the Ag homogeneous sample.
Fig. 1 shows a montage of images corresponding to different
processing techniques and parameter variations. For example,
Fig. 1a shows a single raw image and it is evident that the noise
in the image is higher compared to the rest of the images, for
example Fig. 1f which shows the average 100 reference image.
However, it is much more difficult to discern the differences in
the noise content between the other images. Here is where the
PSNR values become very useful and also allows for a quanti-
tative measure. One thing to note is that the images have
horizontal lines which seem to have higher intensity than its
neighboring lines. This is a direct result of having different
responses from different pixels in the camera. In the push-
broom imaging approach the image is scanned over the same
column of pixels on the camera until there are enough row
elements to give a 2D monochromatic image. Thus, any
response variation of the camera pixels within such column will
manifest as differences between rows. This can be corrected by
implementing a at eld correction.8 Otherwise, the pixel-to-
pixel (or in our monochromatic image case row-to-row) varia-
tion can be taken into account when a quantitative calibration
for elemental composition is performed.10 In this study, the raw
images were used such that the row-to-row variation is evident.
Fig. 2 shows the PSNR values when the images obtained by
different processing techniques are compared to the average
100 reference image. It is clear that the worst, or lowest, PSNR
Fig. 1 GDOES emission maps at 338.3 nm of homogeneous Ag film.
(A) single raw image, (B) single image 2D median filter 5
5, (C) 3D
median filter 5
5
5, (D) single image LPG-PCA, (E) image recon-
structed with PC1 & 2 after PCA analysis, and (F) average of 100 images.
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Fig. 2 Peak signal-to-noise ratio (PSNR), for GDOES emission maps at
338.3 nm of homogeneous Ag film, resulting from various denoising
techniques. The average of 100 images was used as the reference
image.
value is displayed by a single raw image. If we were to have only a
single raw image there are several options to improve the PSNR.
One such option is to perform 2D median ltering. In this case
we dene an area of pixels (3
3, 5
5, etc.) and nd the median
value which is used to replace the center pixel. The advantage of
median ltering is that it can remove outliers efficiently so it is
oen used to remove “salt & pepper” noise or hot pixel contri-
butions. Also, it is a simple and computational-cost effective
protocol. It is evident from Fig. 2 that the PSNR values improve a
lot with 2D median ltering. Also, it can be observed that
increasing the size of the pixel area improves the PSNR values,
albeit with diminishing returns of improved PSNR.
More ltering options are accessible when more than one
image is available. For example, one can perform averaging of
the collected images when the subject can be safely assumed to
be the same. In this case, the Ag content of the layer is homo-
geneous in x, y, and z dimensions so it is a reasonable
assumption, thus the pixels in the z dimension are averaged to
denoise the image. It is clear that the PSNR improves greatly
when 3 raw images are averaged. Also, having more images to
average gives a much better PSNR value which is improved by
utilizing 5 or 10 images to average. This result is expected since
it is well known that increasing the number of measurements
improves the precision of a measurement. The advantage of
averaging is that it is a simple and computational-cost effective
protocol. This means that it is fast to implement.
Having more than one image also allows performing median
ltering in three dimensions. The protocol is very similar to the
2D median ltering, except that now there is a volume of pixels,
or voxel, instead of an area of pixels. In here, the volume was
limited to a symmetrical shape which means that it contains the
same number of pixels in x, y, and z. For example, the 3DMF3,
as labeled in Fig. 2, includes 3
3
3 pixels and the median
from those 27 pixels replaces the center pixel. It is clear from
Fig. 2 that the PSNR is greatly improved by use of the 3DMF3,
even more so than using a 2DMF3 which is a result from using
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more near neighbor pixels in the protocol. It is also evident that
increasing the voxel “radius” by one, 3DMF5, results in a greater
improvement in PSNR compared to increasing the pixel square
“radius” by one in the 2DMF approach.
An interesting approach to image denoising is the applica-
tion of PCA. PCA is a multivariate linear data dimensionality
reduction technique that uses eigen vector decomposition to
capture the maximum variance in the data along a set of
orthogonal axes, termed as principal components. A detailed
description of the underlying mathematics can be found
here.18,19 PCA has been previously used to lower the complexity
of large dimensional data and reveal hidden trends, even in case
of spectral datasets.20 The dataset can be denoised aer trans-
formation into the PCA domain, preserving only the most
signicant principal components21 and then retransforming the
data back into the original form. The main idea of performing
PCA on the GDOES datasets is to capture the correlations
related to intensity variation of individual pixels in a single
image as well as along the image slices. Capturing both these
types of correlations simultaneously is possible due to covariance
statistics inherent in PCA. It is assumed that the evolution of
intensity of the pixels (or image as a whole) with depth is
systematic for all the samples used in this study. This is
reasonable as the evolution of pixel intensity will be gradual in
case of sample with both lateral and depth heterogeneity and
constant in case of sample with homogeneous content and
sample with lateral heterogeneity. Therefore, the rst couple of
PCs will capture the bulk of the variance in the dataset. These PCs
will account for all the systematic changes in the evolution of
intensity in the depth slices and this information can be termed
as signal. The rest of the PCs will capture very less variance in the
dataset. The variance captured by these insignicant PCs will
represent random variations in the data set and this can be
termed as noise. By removing the insignicant PCs, the signal-to-
noise ratio can be improved for the GDOES datasets.
In this case, 20 GDOES images of the homogeneous sample
were collected and processed with the PCA protocol mentioned
in the ESI. Fig. 1e shows the reconstructed image when select-
ing only the rst two components. In this case, the rst
component (PC1) captures 99.71% of the variance and the
second component (PC2) captures 0.017% of the variance. The
reconstructed images taking into account only PC1, PC2, PC3,
or PC4 (see ESI, Fig. 2S†) show that PC3 and PC4 give mainly
noise. This is also conrmed by the loading plots (ESI, Fig. 3S†).
Thus, in this case, PC1 and PC2 are enough to capture the
systematic variation and the rest of the PCs can be discarded
because they mainly capture random variation or noise. It can
be observed from Fig. 2 that the increase in PSNR with a PC1 & 2
reconstructed image is the highest compared to the other image
processing.
Recently, PCA has been applied to single images for denoising
purposes in a technique called local pixel grouping PCA.22 In this
case, a pixel of interest and its neighbors are represented by a
vector variable. Then, pixels with similar local structure to the
one in question are grouped to serve as training sets for the
variable. This is achieved by a method called block matching,
typically used to track motion in video.23 In general, block
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matching relies on computing the sum of the squared differences
(SSD) between the original block, containing the pixel of interest,
and the comparison block. The blocks with the least SSD are the
matching training sets. In this fashion, the following PCA
denoising can better preserve the edge features. For further
details on the LPG-PCA protocol please refer to Zhang et al.22 It is
evident from Fig. 2 that the LPG-PCA protocol provides very good
PSNR over the raw image and most other processing methods in
the comparison. Also, looking back at Fig. 1g (LPG-PCA) it can be
observed that the row-to-row variation is somewhat smeared
which suggests a loss in lateral resolution.
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(b) Images from samples with lateral heterogeneity
The second case (b) pertains to denoising images from samples
with lateral heterogeneity. GDOES elemental mapping relies on
distinguishing the lateral composition heterogeneity and the
noise components can be limiting. Denoising techniques would
potentially allow for an improvement of image quality. The
previous section showcased which protocols give the best PSNR
improvements. However, this section will allow us to determine
if the denoising protocols of interest come at the loss of lateral
resolution. For this purpose, an Ag thin lm sample on a Cu
substrate was perforated to reveal the substrate and have a
laterally heterogeneous sample. Ten GDOES images of such
sample were acquired and the denoising techniques which gave
the best PSNR improvements were applied. Fig. 3 shows a
montage of selected images from this process. To help quantify
the loss of lateral resolution a prole of the Cu 324.7 nm
emission (row of the image) going through the bright spot was
extracted from each image (Fig. 4c). In addition, a Lorentzian
Fig. 3 GDOES emission maps at 324.7 nm of a perforated Ag film on a
Cu substrate. (A) single raw image, (B) single image 2D median filter 7

7, (C) 3D median filter 5
5
5, (D) single image LPG-PCA, (E) image
reconstructed with PC1 & 2 after PCA analysis, and (F) average of 10
images.
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curve was tted, as proposed by Webb et al.,11 to the data and
the full width at half maximum (FWHM) was obtained and used
to measure lateral resolution degradation (Fig. 4d).
It is evident that the lateral resolution degrades (increased
FWHM) particularly in the denoising schemes that incorporate
some sort of lateral grouping of pixels. The largest value of
FWHM resulted from the LPG-PCA protocol and the loss of
lateral resolution is evident by visual comparison of the GDOES
emission image (Fig. 3d) to the rest of the images (Fig. 3). In the
case of the 2D median lter, the 3
3 grouping showed sub-
pixel increase in FWHM. However, increasing the pixel
grouping to 5
5, 7
7, and 9
9, resulted in an increased
FWHM by 1 pixel, 2.8 pixels, and 6.8 pixels, which corre-
sponds to a relative increase of 8%, 22%, and 53%, respectively.
It is clear that the 7
7 and 9
9 2DMF result in an unac-
ceptable loss in lateral resolution. The loss in resolution caused
by the 5
5 2DMF is signicant but its use can still be
considered in a case-by-case basis. The 3
3 2DMF yields
higher delity images but one has to also consider that the
improvement in PSNR was not as high as other methods.
Having more than one image allows the implementation of
the other techniques cited above. The simplest averaging in the
z-dimension produces large increases in PSNR, as shown above,
while maintaining the lateral resolution (Fig. 4d). It should be
kept in mind that the lateral heterogeneity of the sample should
not change between the averaged images.
The 3DMF protocol also yields higher delity. When the
voxel is 3
3
3 the increase in FWHM is 0.1 pixel, and for
the 5
5
5 case it is 0.3 pixels. This is a minimal loss in
resolution which comes with a great increase in PSNR, as seen
in the section above. Again, the great advantage of the 3D
median lter protocol is that it can be applied with low
computational cost.
The PCA was again amongst the best performers. Principal
component 1 captured 98.38% of the variance, while PC2
captured 0.1880%. The loadings plots (see ESI, Fig. 4S†) show
that most of the variance has a random character for PC3 and
PC4. This was observed for the images reconstructed from the
individual principal components up to PC4 (see ESI, Fig. 5S†).
Thus, PC1 and PC2 were both used to reconstruct the image
seen in Fig. 3f. It even showed an observable improvement in
spatial resolution, or a decrease in FWHM. This is evident from
comparison of the raw data prole to the prole from the
reconstructed image aer PCA (Fig. 4c). This is a noteworthy
aspect because spatial resolution refers to the ability to distin-
guish between structures at a given level of contrast. In this
fashion, the signal-to-noise ratio can limit the spatial resolu-
tion. Thus, depending on how poor is the SNR, denoised images
can result in an improved spatial resolution provided no blur-
ring is introduced by the denoising technique, which is
demonstrated by the PCA results.
(c) Images from samples with lateral and depth
heterogeneity
The third case (c) pertains to denoising samples with three-
dimensional heterogeneity. In this case, noise in the depth
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Fig. 4 (A) Topographical profile of perforated Ag film on Cu substrate. (B) Topographical map of perforated Ag film on Cu substrate. (C)
Horizontal emission profiles at 324.7 nm through center of bright spot. (D) FWHM of Lorentzian fits through the emission profiles through center
of bright spot.
dimension, or the random variability from image to image,
would compromise the GDOES depth resolution. Thus,
denoising techniques would potentially help to improve the
ability to distinguish between neighbor layers in depth.
However, as seen above, some denoising protocols come at a
premium of resolution. The effect of denoising on depth reso-
lution was tested in this part of the study by performing a 3D
qualitative GDOES elemental mapping, at 341.5 nm, of a Ni
substrate coated with a thin Cu lm which was in turn perfo-
rated to include a lateral heterogeneity feature.
Fig. 5a shows a 3D GDOES elemental map where 100 raw 2D
GDOES images obtained at sequential sputtering times are
stacked in the z dimension (the top of the stack represents the
surface of the sample or time zero). The pixels with intensities
lower than a threshold given by the measured background are
transparent. In addition, the 341.5 nm emission captured by the
rest of the pixels is plotted in different colors according to the
intensity (dark blue ¼ lowest, yellow ¼ highest). Imaging of a
sample with no lateral or depth heterogeneity would give a
cylindrical colored volume in the region where the GDOES
emission is captured. In our case, the colored volume is not
symmetric at rst because of the lateral and depth heteroge-
neity, but eventually it becomes cylindrical. The volume is a
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similar blue color at the surface because the emission is
dominated by lower values. This can be compared to the blue
pixels sparingly distributed outside of the GDOES emission
volume as a result of the random noise. Fig. 5b shows a vertical
slice through the GDOES 3D qualitative elemental map. The
perforation in the Cu lm can be clearly seen toward the top-
center part of the slice. It is also very clear that the Ni emis-
sion in the le part of the slice begins closer to the surface
compared to the right part of the slice, which is a result of
having a Cu thin lm which varies in thickness across the
mapped volume.
A pixel at (295 265), in the area where the Ni emission begins
to increase closer to the surface, was chosen to obtain a depth
prole for comparing the raw data to the denoised data (Fig. 6).
Only the rst 25 images of the 3D emission map were used for
this purpose to include the region where the emission changes
more abruptly in the depth dimension and to keep the PCA
processing time to a minimum. In this case, only the three
protocols that showed the best denoising while maintaining
lateral resolution were used: z-moving AVG, 3DMF, and PCA. It
is evident from Fig. 6 that all three denoising processes yield
improved data quality with respect to noise. However, it seems
that the change in emission as a function of depth is not sharp
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enough to assess the effects on depth resolution. Thus, a model

3D GDOES depth prole was created to represent the resulting
3D elemental map of a sample with a very thin marker layer.
This was achieved by using the background subtracted average
of the 100 images taken from the homogeneous Ag sample in
Section a (Fig. 1f) and using it as the mean of a Gaussian shape
depth prole. A Gaussian distribution has been previously
observed in GDOES depth proles.24 Furthermore, noise was
added to the model 3D elemental map, with a Gaussian distri-
bution character, to mimic the noise observed in real images.
Such sort of noise would be representative of for example, read-
out noise from the CCD camera.25 Fig. 7 shows the corre-
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sponding volume plot (a) and slice (b). A depth prole through
pixel (185 277), in the center of the GDOES emission map
(Fig. 8), reveals that the averaging approach comes with an
unacceptable premium of depth resolution. The 3DMF
approach gives much better results, with no observable depth
resolution degradation. The 5
5
5 voxel shows slightly
better performance than the 3
3
3 voxel evidenced by the
higher peak value. Finally, the PCA yields the best results again

Fig. 5 (A) Qualitative 3D GDOES emission map at 341.5 nm from

heterogeneous Cu film on Ni substrate. (B) Plane slice across quali-
tative 3D GDOES map in (A).

Fig. 6 Comparison of qualitative depth profile (emission at 341.5 nm Fig. 7 (A) Model qualitative 3D GDOES emission map with a Gaussian
extracted from pixel (295 265), for the first 25 sequential images) intensity distribution in depth and added Gaussian noise (mean values
before and after different denoising techniques. Raw data (solid line), taken from background subtracted Fig. 1I). (B) Plane slice across model
PCA (dotted line), 3DMF5 (dashed line), AVG10 (squares). qualitative 3D GDOES map in (A).

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Fig. 8 Comparison of qualitative depth profile of model data in Fig. 7
before and after different denoising techniques. Model data (solid line),
PCA (dotted line), 3DMF5 (dashed line), AVG10 (squares).
through not only a higher peak value but also an observable
narrower peak which results in discernible spatial resolution
(FWHM) improvement.
Conclusions
It is clear that for homogeneous samples, such as standard
reference materials (SRMs), 2DMF ltering gives desired
improvement in PSNR, without the computational costs of LPG-
PCA, when a single image is available. However, if multiple
images are available, PCA gives better PSNR improvements, but
average or median ltering techniques require minimal
computational cost and can provide very good denoising
provided with enough images.
In the case of laterally heterogeneous samples, if there is
only a single image, one can turn to 2D pixel grouping tech-
niques but at a cost of lateral resolution in such a way that
further gains in PSNR would result in greater loss of lateral
resolution. On the other hand, if multiple images are available,
PCA and depth averaging do not result in a noticeable loss of
lateral resolution, while 3DMF only gives sub-pixel lateral
resolution degradation, as measured by tted Lorentzian
FWHM. Again, provided with enough images the depth aver-
aging should give sufficient gains in PSNR at a minimal
computational cost.
When the sample is heterogeneous in three dimensions one
will have a multiple image case but with systematic changes
from image to image. It is clear that when the systematic
changes are very sharp the depth averaging degrades the depth
resolution. Once again, PCA shows the best results but with a
premium of computational cost. In this case, 3DMF can prove to
be very useful because it can give signicant PSNR gains with
minimal-to-no degradation in spatial resolution while being
highly computational-cost efficient.
Overall, averaging in the z dimension or performing 3D
median ltering (depending on the expected heterogeneity) is
recommended when computational costs are to be kept at a
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minimum and there are enough images to obtain the desired
gain in PSNR. On the other hand, PCA is recommended when
computational costs are of minimal concern because it will
yield the best results. In addition, in the present study only
monochromatic maps were considered but a hyper-spectral
data cube was in fact collected for a wide wavelength range
and PCA presents the opportunity of discovering patterns
hidden by the data complexity. This is an avenue which the
authors are currently pursuing.
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