Facies
DOI 10.1007/s10347-013-0383-z
ORIGINAL ARTICLE
Digital image treatment applied to ichnological analysis of marine
core sediments
Javier Dorador • Francisco J. Rodrı́guez-Tovar
IODP Expedition 339 Scientists
•
Received: 13 August 2013 / Accepted: 5 October 2013
Ó Springer-Verlag Berlin Heidelberg 2013
Abstract Characterization of trace fossils in marine core
sediments is, most times, difficult due to the weak differentiation between biogenic structures and the host sediment, especially in pelagic and hemipelagic facies. This
problem is accentuated where a high degree of bioturbation
is associated with composite ichnofabrics. Simple methods
are presented here based on modifications to image features
such as contrast, brightness, vibrance, saturation, exposure,
lightness, and color balance using the software Adobe
Photoshop CS6 (Adobe Systems, San Jose, CA, USA) to
enhance visibility and thus allow for a better identification
of the trace fossils. Adjustments involving brightness,
levels and vibrance generally give better results. This
approach was applied to marine cores of pelagic and
hemipelagic sediments obtained from the Integrated Ocean
Drilling Program Expedition 339, Site U1385. Enhancing
the digital images facilitates ichnological analysis through
improving the visibility of weakly observed trace fossils,
and in some cases revealing traces not detected previously.
IODP Expedition 339 Scientists: Hernández-Molina F.J., Stow
D.A.V., Alvarez-Zarikian C., Acton G., Bahr A., Balestra B., Ducassou
E., Flood R., Flores J.-A., Furota S., Grunert P., Hodell D., JimenezEspejo F., Kim J.K., Krissek L., Kuroda J., Li B., Llave E., Lofi J.,
Lourens L., Miller M., Nanayama F., Nishida N., Richter C., Roque C.,
Pereira H., Sanchez Goñi M., Sierro Sanchez F., Singh A., Sloss C.,
Takashimizu Y., Tzanova A., Voelker A., Williams T., Xuan C.
J. Dorador F. J. Rodrı́guez-Tovar (&)
Departamento de Estratigrafı́a y Paleontologı́a, Universidad de
Granada, 18002 Granada, Spain
e-mail: [email protected]
J. Dorador
e-mail: [email protected]
Keywords Ichnological analysis Digital images
treatment Marine core deposits Integrated Ocean
Drilling Program Expedition 339 Site U1385
Introduction
Ichnological analysis has shown itself to be very useful,
particularly since the onset of the 21st century, in different
fields of the Earth Sciences, with special applications in
paleoecology, basin analysis, and reservoir characterization
(e.g., Pemberton et al. 2001; McIlroy 2004; Buatois and
Mángano 2011; Knaust and Bromley 2012). Trace fossils,
representing evidence of an organism’s behavior, provide
valuable information on the depositional and ecological
parameters that determine variations in the ethology of the
producer. Hence, trace fossils can reveal the response of
trace-makers to environmental factors such as hydrodynamic energy, sedimentation rate, oxygenation, salinity,
temperature, organic matter, and bathymetry (e.g., Buatois
and Mángano 2011). Although ichnological research has
undergone rapid growth in the last decade, there are limitations, especially when working with core material. The
particular features of cores, their limited size, restricted
surface, scarcity of horizontal or bedding planes, the near
exclusiveness of two-dimensional expression of trace fossils, make ichnological analysis difficult (e.g., Bromley
1996; Gerard and Bromley 2008; Knaust 2012).
Since the second half of the 20th century, a number of
different techniques have been applied to improve the
visibility and identification of trace fossils in core sediments. X-rays were first applied in the 1960s (Bouma 1964;
Howard 1968) and have been extensively used in recent
decades (e.g., Grimm et al. 1996; Löwemark and Werner
2001), with excellent results, even allowing 3D
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Facies
reconstructions of biogenic structures (Löwemark 2003;
Löwemark and Schäfer 2003). In the wake of this comparatively straightforward method, more complex techniques have included computed tomography (CT) (e.g.,
Joschko et al. 1991; Dufour et al. 2005; Rosenberg et al.
2007; Davey et al. 2011), magnetic resonance (Gingras
et al. 2002a, 2002b), and multi-stripe laser triangulation
(MLT) (Platt et al. 2010). These techniques have provided
3D reconstructions of trace fossils, which may give valuable information on orientation and cross-cutting relationships, but they are expensive and the necessary instruments
may be inaccessible.
To solve problems surrounding accessibility, cost, or
availability of core material, one sound option is to work
with the digital images, highlighting the differences
between trace fossils and host sediment to identify the
biogenic structures better. This approach was initiated in
the 1990s by Magwood and Ekdale (1994), applying
mathematical equations and convolutions to one original
image to attain a higher contrast between traces and host
sediment. After this first application, however, its development was stagnant for many years. Then, Honeycutt and
Plotnick (2008) applied image analysis for the calculation
of bioturbation indices, based on the difference between
grey-scale pixels. The method, relying on software that
automatically selects biogenic structures, is useful to
determine bioturbation indices when a clear difference
exists between trace fossils and the host sediment. Meanwhile, Qi et al. (2008) used image processing in complex
ichnofabrics to focus on parameters such as color, contrast
direction, and internal structure.
The aim of the present study is to advance the application of digital imagery to ichnological analysis, providing a thorough but easy-to-use means of enhancing trace
fossil visibility, especially useful for core material. By
using Adobe Photoshop CS6 software, numerous parameters can be modified, and the most appropriate ones for the
study at hand can be selected. This method, which is
cheaper and easier to use that those proposed previously,
can be applied by non-specialists in digital image
processing.
Materials and methods
Studied material
Digital image treatment was conducted on high-resolution
images from marine cores obtained during IODP Expedition 339 that took place in the Gulf of Cádiz and off west
Iberia from November 2011 to January 2012 (Expedition
339 Scientists 2013a). From the studied sites, Site U1385,
located off southwest Portugal (37°34.2850 N; 10°7.5620 W),
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was selected due to its significance for interpreting global
environmental conditions (Site U1385 is close to the wellknown ‘‘Shackleton Site’’). The core material consisted of
hemipelagic–pelagic continental margin sediments, mainly
composed of mud and clays (Expedition 339 Scientists
2013b). Selected intervals in the core were chosen for
research as a result of the relatively poor visual differentiation between trace fossils and host material.
Methodology
To develop a digital image methodology useful for the
specialist, but at the same allowing for generalized use,
several steps were taken:
1.
2.
3.
First, a variety of adjustments (brightness, levels,
curves, exposure, vibrance, hue/saturation, and color
balance; in italics for their identification as adjustments) were tested on digital images in order to
analyze their usefulness for improving the visibility of
trace fossils. These adjustments, made using Adobe
Photoshop CS6 software, had a variable effect on some
image features, such as contrast, brightness, vibrance,
saturation, exposure, lightness, and color balance.
After application to numerous and often different
cases, with variations in the ichnological (e.g., types of
traces, size, filling material, diffusiveness) and sedimentological features (lithology, grain size, color,
etc.), the most useful adjustments were selected
depending on the particular case.
Selected adjustments were sequentially applied to
several different cases, changing the values of these
adjustments to evaluate the range of values inducing
higher visibility in view of particular features.
Adjustments
The tested adjustments showed different capabilities in the
modification of image features, making their utility variable. The adjustment characteristics are as follows:
Brightness This adjustment controls the amount of light
that is reflected and serves to correct very dark or light
images after levels modification, and can also increase the
contrast through the modification of that parameter.
Brightness entails modification of two parameters, contrast
(from -50 to 100) and brightness (from -150 to 150).
These values are numbers internal to the used software, as
variation from the value of the original image, represented
by 0. Higher contrast values increase the difference
between pixels and improve visibility of the trace fossil.
Brightness allows the light reflected by the image to be
modified, thereby improving visibility when working with
Facies
images that are too dark or too light. Brightness could be
especially desirable to increase tone differences in the
study of marine cores where there is weak color difference
between traces and host sediment.
usually the case in core research. However, its application
in grey tone images, frequently encountered in core
research, makes it possible to eliminate yellowish tones that
may result from previous adjustments during the procedure.
Levels This adjustment, which stretches the histogram of
pixel values, increases the differences between pixels. This
is an interesting adjustment that enables one to crop out the
pixel histogram and cast aside pixel values that do not
appear in the image. Moreover, applying this adjustment,
contrast is increased when the histogram is stretched.
Levels adjustment is easy to execute because the software
shows a graphic histogram, and one only needs to change
the limits (0–255) until reaching the pixels that are in the
image. These limits consist of black and white levels, but
the grey level in the middle of the histogram can also be
changed. The default grey level value is ‘‘1’’ but by
increasing or decreasing this value, the image becomes
lighter or darker, respectively. This adjustment is very
useful for core images: the pixel values that are not located
in the image can be dismissed, by histogram stretching, so
that the contrast indirectly increases. This indirect change
in contrast can also be achieved through the application of
other adjustments (curves and exposure), but in a more
complex way.
Hue/saturation This adjustment leads to modification of
colors based on the control of three parameters, hue, saturation, and lightness. Hue parameter is modified using a
sliding color bar where a particular color can be selected,
and then the original ones change towards the selected
color. There are situations where the visibility of some
traces is slightly improved when tone is changed with the
hue adjustment (especially with green or blue). After that,
the saturation and lightness of the selected tone can be
changed by the modification of the other two adjustments
(saturation and lightness).
Curves This adjustment allows for a change in levels in a
more complete way because it is possible to modify
shadows, midtones, and highlights independently. When
selecting this adjustment, the software shows a diagram
with the histogram in the background and a diagonal line
that crosses it in the foreground and that can be modified.
Changes conducted on the line serve to control the shadows
(bottom of the line), highlights (top of the line), and midtones (middle of the line). This tool is similar to the levels
adjustment and has even more options, but its application is
more difficult.
Exposure Exposure also resembles the two previous
adjustments (levels and curves), and is based on modification of three parameter bars (exposure, offset, and
gamma correction). The exposure parameter bar increases
the general brightness and thereby all tones are modified,
whereas the offset parameter bar controls the shadows, and
the gamma correction parameter bar modifies the midtones.
Vibrance This adjustment allows us to modify the yellow
tones and turn the image to less artificial grey tones.
Vibrance controls the saturation of colors with the modification of two parameters, vibrance and saturation, with
values from -100 to ?100. These two parameters are
especially useful for brightly colored images, which is not
Color balance This allows particular colors to be generalized and for luminosity to be maintained in the threetone range of the image (shadows, midtones, and highlights). Cyan-red, magenta-green, and yellow-blue are the
pairs of colors that can be increased, corresponding to the
three color channels R (red), G (green), and B (blue),
respectively. This adjustment allows a check on whether
the visibility can be improved when different color filters
(cyan, red, magenta, green, yellow, or blue) are applied.
Adjustment selection
Levels, brightness, curves, exposure, vibrance, hue/saturation, and color balance were tested in several images,
selecting those adjustments that improved the visibility of
trace fossils with respect to the host sediment.
According to the results obtained, levels, brightness, and
vibrance adjustments were selected as the most useful
because they clearly increased the visibility of trace fossils,
while the remainder of the adjustments, curves, exposure,
hue/saturation, and color balance, were not considered in
the final method as a result of the comparative complexity
and/or limited improvement of trace-fossil visibility. Hue/
saturation adjustment was less useful in grey tone images;
it makes color modifications that do not improve the visibility while resolution decreases substantially; thus, its use
is not recommended, and color balances were not included
in the presented method because different combinations
were checked and the visibility was not clearly modified.
Technique
After selection of the most useful adjustments, the procedure applied to the core images consisted of the following
sequential steps: (1) levels were applied to an image to drop
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Facies
the histogram and improve the contrast, (2) the brightness
adjustment was applied to increase the contrast and control
the brightness, and finally, (3) vibrance was applied to
make slight modifications. This sequence was repeated for
selected images (38 full cores and ten intervals).
The full procedure was executed in every image, and we
analyzed the values obtained for each parameter, represented in a box-plot graph (Fig. 1), having chosen the most
appropriate range according to the particular case.
The levels adjustment depends on maximum and minimum pixel values that are represented in the image, the
maximum corresponding to the black value and the minimum to the white one. The average white value was 54.3,
with a minimum of 24 and maximum of 89, whereas the
black value had a mean value of 100, ranging from 88 to
131 (Fig. 1). Finally, the grey level was commonly modified to bring out the dark tones of the image and make the
image slightly darker. Images were generally modified to
darker tones because it was very difficult to study and
identify trace fossils in light images as a result of the
amount of light they reflected. The maximum value was 1,
and the minimum value was 0.19, with a mean of 0.76
(Fig. 1). White and black values represent the minimum
and maximum pixels, respectively, in each image, and grey
corresponds to a value internal of this software with values
of 10 in black and 0.01 in white. Applying this adjustment,
the contrast is increased as the histogram of pixel values is
lowered according to the values in the original image.
Using the brightness adjustment, the contrast and
brightness parameters were modified until arriving at the
best possible combination for a better visibility of trace
fossils. The first parameter modified was contrast, consistently showing positive values, usually higher than 50; the
mean was 70, with a minimum of 26 and a maximum of 93
(Fig. 1). The second parameter was brightness, with a
minimum value of -63, maximum of ?51, and an average
of -8. The values used in the brightness adjustment represent the variation from the original value of the modified
Fig. 1 Ranges of parameter
values of each adjustment. Boxplot of modified adjustments
(levels, brightness, and
vibrance) and the corresponding
parameters (white, grey, and
black for levels; brightness and
contrast for brightness; and
vibrance and saturation for
vibrance). Values of any
parameter are indicated by a box
that is defined by first and third
quartiles, a line inside the box
representing the median, and
two external short lines
corresponding to 0.95 and 0.05
values
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image, obtained after the application of the first adjustment,
represented by 0. In this second modification, the contrast
is slightly increased and the amount of light that is reflected
is controlled by the brightness adjustment.
The vibrance adjustment modifies the intensity and
saturation of the image; it was tested and modified until
obtaining the best possible image. To eliminate the yellowish tones in the images, caused by previous adjustments, the two parameters of this adjustment (vibrance and
saturation) were applied with negative values (Fig. 1).
Saturation was less variable with an average value of -66
(with -87 and -50 as minimum and maximum, respectively), whereas vibrance, sensu stricto, had a mean value
of -31 (-90 and ?20 as minimum and maximum). The
values represent the same as in the previous adjustment;
variation from the original value of the modified image,
obtained after two previous adjustments.
Results and discussion
To evaluate the usefulness of this digital image treatment,
two main situations were selected from the numerous
studied cases: (1) Dark trace fossils with lighter host sediment, and (2) light trace fossils surrounded by darker host
sediment.
Dark trace fossils and lighter host sediment
An example where dark trace fossils are observed surrounded by lighter host sediment is seen in core U1385E16H from 24 to 30 cm. Directly in the high-resolution
original image, a horizontal trace fossil can be seen, though
scarcely differentiated from the host sediment (Fig. 2a).
Firstly, the levels adjustment was executed with values of
65, 0.74, and 102 in the white, grey, and black levels,
respectively. After this adjustment (Fig. 2b), the horizontal
trace that was weakly observed could be clearly seen, even
Facies
Fig. 2 a Original image of U1385E-16H in the interval 2 from 24 to 30 cm, b image after application of levels adjustment, c image adding
brightness adjustment, and d image adding vibrance adjustment. Pl (Planolites); Tae (Taenidium); Th (Thalassinoides)
showing a clear internal structure, suggesting a possible
assignation to Taenidium. Some other traces fossils, probably Thalassinoides (at the top and in the bottom left
corner), and some Planolites become apparent. Application
of the brightness adjustment (Fig. 2c), with brightness 17
and contrast 91, provided for better visualization of the
trace fossils recorded in the lower part. The yellowish tone
of the image after the application of the brightness
adjustment was corrected with the vibrance adjustment
(Fig. 2d), vibrance -50 and saturation -70 producing the
best visualization of the trace-fossil assemblage.
Light trace fossils and darker host sediment
Light trace fossils surrounded by darker host sediment are
illustrated in core U1385A-4H, from 54 to 59 cm (Fig. 3a).
The high-resolution digital image shows only a horizontal
trace and a slightly circular burrow; internal structures are
not observed precluding any ichnotaxonomical classification. Levels adjustment was applied to the limits of the
histogram 48-0.71-112, white, grey, and black levels,
respectively; some internal structures become visible and
several new trace fossils appear for the first time, at the top
and bottom of the image (Fig. 3b). Brightness adjustment
was applied to modify the contrast, increased up to 88. The
brightness parameter was not modified, because in images
with light trace fossils such as this (Fig. 3c), increased
brightness induces a lighter color of the host sediment and
thus less visibility of the trace fossil. After application of
brightness adjustment, the visibility of the trace fossils and
their internal structures improve; a halo is even distinguished in the trace fossil located in the middle of the
image, allowing its ichnotaxonomical assignation to Palaeophycus. Finally, a vibrance adjustment was executed
with a vibrance value of -41 and a saturation value of -72
to lend to the image grey tones and correct the orange tone
introduced by the previous adjustments (Fig. 3d). The final
image reveals a clear internal structure in the horizontal
trace initially observed, allowing its assignation to Zoophycos; this is supported by similar, semi-parallel structures located above, now first discerned. Moreover, the
previously differentiated Palaeophycus can be clearly
identified because its halo is now well visualized, and two
other trace fossils are clearly observed and identified as
Thalassinoides.
Conclusions
1.
2.
The digital image treatment described here has been
applied to core sediments from the IODP Expedition
339, Site U1385, allowing modifications in certain
image features such as contrast, brightness, vibrance,
saturation, exposure, lightness, and color balance to
enhance visibility and thus enable a better identification of trace fossils.
After application of several adjustments (brightness,
levels, curves, exposure, vibrance, hue/saturation, and
color balance), levels, brightness and vibrance were
found to be the most useful in the studied cases.
Fig. 3 a Original image of U1385A-4H in the interval 7 from 54 to 59 cm, b image after application of levels adjustment, c image adding
brightness adjustment, and d image adding vibrance adjustment. Pa (Palaeophycus); Th (Thalassinoides); Zo (Zoophycos)
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Facies
3.
4.
5.
Better results have been obtained following a procedure consisting of three sequential steps: (1) levels
were applied to an image to reduce the histogram and
improve the contrast, (2) brightness adjustment was
applied to increase the contrast and control the
brightness, and (3) vibrance was used to make slight
modifications.
Application to core sediments from the IODP Expedition 339, Site U1385, provided enhanced visibility of
weakly observed trace fossils in the high-resolution
digital images, including internal structures, and this
made it possible to visualize, for the first time, new
trace fossils.
The method described here is quick and easy to apply,
even for non-specialists in digital image analysis,
making it promising for generalized use.
Acknowledgments This research used samples and/or data provided by the Integrated Ocean Drilling Program (IODP). Funding for
this research was provided by Project CGL2012-33281 (Secretarı́a de
Estado de I ? D ? I, Spain), and Project RNM-3715 and Research
Group RNM-178 (Junta de Andalucı́a). The research of JD was
financed with a pre-doctoral grant supported by the University of
Granada. Editor Maurice Tucker and the two reviewers (Drs. Dirk
Knaust and Ludwig Löwemark), provided useful comments and
suggestions.
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