Journal of Threatened Taxa |
www.threatenedtaxa.org | 26 January 2020 | 12(1): 15173–15180
ISSN 0974-7907 (Online) | ISSN 0974-7893
(Print)
doi: https://doi.org/10.11609/jott.5041.12.1.15173-15180
#5041 | Received 02 May 2019 | Final received
09 January 2020 | Finally accepted 13 January 2020
Digital image post processing
techniques for taxonomic publications with reference to insects
Nikhil Joshi 1, Hemant
Ghate 2 & Sameer Padhye
3
1,2 Post-Graduate Research Centre,
Department of Zoology, Modern College of Arts, Science and Commerce,
Shivajinagar, Pune, Maharashtra 411005, India.
3 Zoo Outreach Organization, No.
12, Thiruvannamalai Nagar, Saravanampatti-Kalapatti
Road, Saravanampatti, Coimbatore, Tamil
Nadu 641035, India.
1 niksjoshi20@gmail.com, 2 hemantghate@gmail.com,
3 sameer.m.padhye@gmail.com (corresponding author)
Abstract: There exists substantial
literature for capturing digital images of insect specimens for taxonomy
purposes but very few papers are available on post processing of these
images. We present a few techniques for
editing digital images of insects using Adobe® Photoshop®
which can be performed in a relatively short amount of time. The results clearly show that techniques
using a combination of options like Curves, Dodge/Burn, Hue/Saturation and Lab Color mode in the software, enhance the quality of the
original image without changing any taxonomic information. These methods applied in different
combinations can be used for taxonomy of any insect taxon. We also caution the readers of the abuse of
such techniques in context of taxonomy.
Keywords: Adobe® Photoshop®,
beetles, insects, lab color, purple fringing.
Editor: Mandar Paingankar,
Government Science College, Gadchiroli, India. Date
of publication: 26 January 2020 (online & print)
Citation: Joshi, N., H. Ghate & S. Padhye (2020). Digital image post processing
techniques for taxonomic publications with reference to insects Journal of Threatened Taxa 12(1): 15173–15180. https://doi.org/10.11609/jott.5041.12.1.15173-15180
Copyright: © Joshi et al. 2020. Creative Commons Attribution
4.0 International License. JoTT allows unrestricted use, reproduction, and
distribution of this article in any medium by providing adequate credit to the
author(s) and the source of publication.
Funding: No funding
was received for this work.
Competing interests: The authors
declare no competing interests.
Author details: Nikhil Joshi is an independent researcher
working on taxonomy and ecology of heteropteran insects of Western Ghats of
Maharashtra. Hemant Ghate
is a former Head of Department of Zoology of Modern College of Arts, Science
and Commerce, Shivajinagar, Pune. Currently working on bugs at Post graduate
research center of Modern College, Pune.
Sameer Padhye
currently works with Zoo Outreach Organization on freshwater invertebrate
diversity and certain aspects of community ecology. His interests include
branchiopod crustacean taxonomy and systematics, taxonomical and functional
diversity patterns of invertebrate species communities found in freshwater rock
pools and eutrophicated water bodies.
Author contribution: SP and HG conceptualized the
idea. HG and SP carried out photography. NJ and SP carried out the
post-processing of images. All authors contributed to writing the manuscript.
Attribution statement: Adobe® Photoshop® is a registered
trademark of Adobe Systems Incorporated in the United States and/or other
countries.
Acknowledgements: The Authors thank the Zoology
Department, Modern College, Shivajinagar, Pune, for providing the lab space
required for the work. SMP thanks Sanjay
Molur and Zoo Outreach Organization for their
support. Authors are grateful to the
editors for betterment of the article.
Introduction
Insect taxonomy using some/any
kind of illustrations to support descriptions has always made it easier for the
reader to comprehend those descriptions.
The form of illustrations has evolved from simple drawings used in early
studies to the use of digital imaging via confocal microscopy, scanning
electron microscopy, dual beam scanning electron microscopy, and micro-CT
(among others) for studying and describing specific aspects of their morphology
(Wipfler et al. 2016).
By and large though, images (and
drawings) taken by digital cameras with/without use of stereomicroscopes and/or
bright field compound microscopes are widely used in insect taxonomy currently
(Buffington et al. 2005; Holzenthal 2008). Digital imaging systems and techniques such
as the ‘Auto Montage’ (hardware and software) (Azorsa
& Sosa-Calvo 2008; Jansen & Halbert 2016; Otto 2016), ‘Dome lighting’
(hardware) (Kerr et al. 2008) and ‘Natural color 3D
models’ (hardware and software) (Nguyen et al. 2014) are now utilized for
documentation and taxonomic studies of various insects.
Subsequently, many softwares are available to cater to the processing of such
captured images (e.g., Adobe® Photoshop® and GIMP). These provide a plethora of tools and
techniques for different aspects of image editing. Using these tools, Jakubec et al. (2018) have provided an excellent and less
time consuming method which is used for background isolation of the
entomological digital illustrations.
While literature exists detailing various methods of photo documentation
for different insect groups (Häuser et al. 2005;
Riedel 2005; Buffington & Gates 2008), to our knowledge, not much
literature exists for the image processing details in context of taxonomy. The
best example we know of are the image editing procedures explained on the
journal, ‘Zootaxa’ website (http://mapress.com/zootaxa/imaging/index.html).
With this background, we present
a few digital image processing techniques by using Adobe® Photoshop®
which can be done in a relatively less amount of time using Coleoptera (images) as a model system.
Materials
and Methods
Material studied
Species from four families of Coleoptera, viz., Cerambycidae, Chrysomelidae, Dytiscidae, and Endomychidae were used for standardizing the different
image editing processes. Selection of
the insect group was based solely on the availability of specimens, no other
selection criterion was used.
Methods
Multiple images were taken either
via 1) Canon 400D SLR camera with a 100mm macro lens and/or 2) Stereo Binocular
Microscope (Leica MZ6 with attached Canon PowerShot
S50). Multiple images were taken and
digitally stacked using COMBINE ZP (http://www.hadleyweb.pwp.blueyonder.co.uk/),
a freeware. The photo processing
techniques were standardized on Adobe® Photoshop® CS5
student version on Windows 10.
We have explained some of the
basics before the actual procedures (given below), though, absolute essentials
of Adobe® Photoshop® are beyond the scope of this work
and hence, not covered here. Readers who
wish to learn about it can visit the official site for help. Terms and terminologies are as per Adobe®
Photoshop® CS5 software.
We have used only a single
representative image of a cerambycid beetle while describing the processes for
consistency.
Some pre-requisite basics are
first explained below before the actual methods.
1) New Layer
New layer creates a blank space
where in additional colors and vectors can be put and
later merged/blended with the image to be processed. New layer can be created by pressing the
‘Create New Layer’ icon on the bottom right of the main window
(Image 1a ‘circle’) or by going to the ‘Layers’ drop down menu, selecting ‘New’
followed by ‘Layer’. New layer can also
be created by pressing Shift+Ctrl+N.
2) Duplicate Layer
Duplicate Layer makes a copy of
the original image/Layer. This is made
so that the original image is not changed or processed in any way. A Duplicate Layer can be created by going to
the ‘Layers’ drop down menu and selecting ‘Duplicate Layer’. Duplicate Layer can also be made by pressing
Ctrl + J.
3) Adjustment Layer
Adjustment Layers are used to
edit the images and using them is more advantageous as they can be switched
on/off and/or modified later. Adjustment
Layers can be created by pressing the ‘Create Adjustment Layer’ icon located on
the bottom right of the main window (Image 1a ‘square’) or going to the
‘Layers’ drop down menu and selecting ‘New Adjustment Layer’.
4) Layer Mask
A layer mask is created in Adobe®
Photoshop® to either reveal or hide all the details of the
image. A white layer implies all the
details are revealed while a black layer means that all the details are hidden
(Image 1b ‘rectangle’). Layer mask can be made by selecting the ‘Create Layer
Mask’ icon on the bottom right of the main window (Image 1a ‘thick arrow’) or
going to the ‘Layers’ drop down menu, selecting ‘Layer Mask’ and further
selecting either ‘Reveal All’ or ‘Hide All’.
Pressing Alt on the mask displays the actual layer mask (Image 1a &
b).
Image processing techniques
Aligning the image (Image 2a)
Generally, while making
scientific illustrations, it is important to have well aligned images in 90° or
180°. Hence, when the captured image is
not at a desirable position, it can be aligned using the Image Rotation option.
The image can be aligned as per
user specification.
Duplicate the layer
Go to Image > Image Rotation
(Image 2a ‘square’) (Extent of rotation is determined by the user).
2) Lightening or darkening parts
of the image (Image 2b).
Overexposure and/or under
exposure in portions of the images is edited by two tools namely, ‘Burn’
(darkens overexposed parts of the image) and ‘Dodge’ (lightens the dark parts
of the image) respectively (Image 2b ‘Rectangular box’).
Select the option as per the
image exposure
Select the ‘Shadows’ part in the
dropdown menu after selecting ‘Dodge’ (Image 2b ‘thick arrow’) so that only the
darkest parts of the image are highlighted and mid tones are left in their
natural state. Similarly, select the
‘Highlights’ parts in the drop down menu after selecting Burn so that only the
white parts (overexposed) are darkened.
Brush size is selected as per the
area of the image which needs either of the two tools (Image 2b ‘circle’)
Exposure (intensity) of the brush
is selected as per the requirement for the image (Image 2b ‘thin arrow’). A value between fifty to seventy percent
usually works.
3) Adjusting the Levels (Image 3a
& b)
The lighting levels of the photo
can be quickly edited by using ‘Curves’ in the ‘Adjustment Layer’ menu. Levels can also be adjusted by using the
option ‘Levels’ in the ‘Adjustment Layer’ (not explained here).
Select the ‘Curves’ option (Image
3a ‘arrow’) in the ‘Adjustment Layer’.
This will open a graph of the
composition of the image (Image 3b ‘square box’)
Adjust by moving the slider (via
mouse) either in the X or Y axis as required (Image 3b thin and thick arrows’,
respectively)
4) Sharpening (Image 4a & b;
Image 5a & b)
This tool is used when the
details within the image come out soft and need to be emphasized more. Basic sharpening includes using Sharpen tools
in Filter menu (not explained here).
One way of doing effective
sharpening of the image is by a combination of a) Lab color
mode and b) High pass filter
Duplicate the layer
Go to Image pull down menu and
select ‘Mode’ followed by ‘Lab color’ (Image 4a
‘square box & arrow’). A message
will follow this selection for which Don’t flatten should be chosen (Image 4b)
Duplicate this layer again (and
this layer should be selected)
Go to ‘Filter’ and select ‘Other’
followed by ‘High Pass’ (Image 5a ‘square box’)
In the ‘High Pass’ window (Image
5b ‘square’), select the radius; optimum value ranges between 2 and 6 (Image 5b
‘arrow’). Exact value has to be selected
as per the image requirement. Click OK.
Select the ‘Soft Light’ or
‘Overlay’ Blending mode (In the drop down menu below Layers on the Right Hand)
(Image 5b ‘round edged rectangle’)
The two layers should then be
merged (this can be done by selecting the two layers and then pressing Ctrl +
E).
5) Color
artifacts (Image 6 a,b)
The captured image sometimes
contains color artifacts
which alters its original color. Many times, images also have purple fringing
(PF), a chromatic aberration occurring at the edges of the image (especially
when the microscope does not have achromatic lenses). These can be edited by making use of
‘Hue/Saturation’ option in the Adjustment layer in Adobe® Photoshop®
Image must be in RGB mode (if it
has been earlier converted to Lab color)
Duplicate the layer (Ctrl + J)
Go to the ‘Adjustments Layer’ on
the bottom right of the main window (Image 1 ‘square’) and select
‘Hue/Saturation’ (Image 6a ‘rectangle’ & ‘thick arrow’)
In the ‘Adjustment Layer’ window
click on the second drop down menu (Image 6b ‘circle’) and select Magenta/Blue
(for PF) (or the color of the aberration/artifact)
After selecting the color, a Dropper Tool icon will be active located below the
‘Lightness’ slider (Image 6b ‘thick arrow’).
Select the dropper tool and move it to the part on the image which has
the artifact/s.
After selecting it, Photoshop will give a color
range of that color (located below the dropper tool)
(Image 6b ‘thin arrow’) (Re-check if it is the right shade).
Drag the Saturation slider to the
left-hand side till the point the color artifact is not seen anymore (Image 6b ‘rectangle’)
In many cases, it also affects
the natural coloration of animals
What can be done for this?
Make a ‘Layer Mask’ (Image 1a)
Hold the ‘Alt’ key and left click
on the Layer mask to select it (Image 1b)
Press Ctrl + I to convert the
white layer to black (thus hiding all the desaturation done)
Select the Paint brush tool with
white color followed by stroking on the parts which
have purple fringing so that only those parts are edited and show up while the
original color is retained for the rest of the image.
6) Background color
(Image 7 a,b)
This tool is used to get a
uniform background color of choice for any
image. It is ideal for photos taken with
any uniform background.
Please note: For using this tool,
the original background should have fewer colors to
begin with and it is not recommended when the image contains complex
backgrounds (e.g., Live animal in its natural habitat). Chroma+ method can also be used for unifying
background if you have images with chroma background and neutral background. This method is surely less time consuming
when you have images with both chroma+ and neutral backgrounds. If time for capturing image is also
considered, then both chroma+ and below mentioned method consumes equal amount
of time with similar final results.
Create an empty Layer (Image 7a
‘square’) below your image and fill it with White (or the background color of your choice) (Take care that the color selected should not be the same shade of the new
intended color for this method to work. E.g., If the background color
of the original image is green, refrain using any shades of green for the new
intended background) (Image 7a ‘thin and thick arrows’)
Right click on the ‘Eraser’ tool
on the left-hand side panel of Photoshop and select ‘Background Eraser Tool’
(Image 7a ‘rectangle’)
Select ‘sampling once’ from the
sampling tool bar, which is placed next to the ‘brush preset
picker’ (Dropper icon with a bullseye mark) (Image 7b ‘thin arrow’)
Select the ‘Limits’ (for
selecting type of background erasing) as ‘Find Edges’ from the drop down and
set the tolerance between 50–70 % (this value will change as per the image)
(Image 7b ‘thick arrow’)
Start erasing the
background. Just make sure the plus mark
seen in the Brush pointer should be always placed on the background while
clicking not on the image (otherwise any colors
resembling the background in the specimen will also be erased).
Results
and Discussion
The processed images showed a
marked improvement without any loss of taxonomic information. Details which were hidden due to insufficient
light were highlighted clearly using Curves (Image 8a & b) and Dodge tools
(Image 8c & d). The soft parts of
the images were refined noticeably after sharpening, (Image 9a & b) while
the color artifacts were
completely nullified thereby revealing the true color
of the specimen (Image 9c-f). The background of the image was completely
changed bringing more contrast to the image (Image 10a & b). The photos then become very suitable for
taxonomy publications as shown here.
The aforementioned techniques can
be used singly or in combination (E.g., Image 10c & d) as per the
researcher’s requirement for any insect taxon (with slight alterations),
though, image capture techniques need to be selected appropriately beforehand
given the taxa under consideration; for example, the number of images required
for stacking for a beetle would be different than that for a butterfly given their
body convexity (Riedel 2005).
An ideal image is the one which
does not require any or very little processing but that does not happen in many
cases. Many laboratories do not have the
necessary infrastructure due to financial and/or logistical constraints.
Capturing high resolution images optimally in an affordable way poses a
challenge which needs to be tackled (Buffington & Gates 2008). Still, good images can be taken by adjusting
conditions such as correct and/or additional lighting, use of correct lenses
(if using SLR or micro 4/3rd), finest use of manual Mode in digital
cameras and making adequate (not excessive) use of photo processing tools (as
is shown through this study). Simple
tools such as ‘Unsharp Mask’ can help sharpening the
image in Adobe Photoshop (R) as suggested by Zootaxa
(see guidelines for preparing images).
Images or line drawings
considerably improve the contents of the taxonomy papers and providing such
illustrations gives valuable information while describing and/or revising new
species, genera or families; e.g., assassin bugs (Weirauch
et al. 2014), tiger beetles (Moravec 2016), and scarab beetles (Rossini & Vaz-de-Mello 2017).
In spite of the availability of the latest technology people are still
using poor quality images in biology papers in many instances. Preparing good images or drawings is an
important issue in taxonomy and our paper assists in this issue to a certain
extent. This article focuses on post
processing techniques of already existing image while earlier work cited here,
mainly describes procedures for obtaining good quality images. We understand that software would be updated
frequently but all the protocols provided here are basic and would be
functional in the updated versions.
There is a high chance that, all these editing processes will be
automated with the progress in the technology.
We would like to caution the
readers that our aim here was to present ways to process only properly taken
digital images where in altering few aspects such as orientation, background color and exposure betters the already good quality of the
image. These techniques are not meant
for enhancing or editing poorly captured images. We would also like to point out that, even
though the use of good photographs are extremely beneficial and could be used
as substitutes for the type specimens in some cases, they should never replace
actual type specimens (Rogers et al. 2017).
Actual specimens act as replicable datasets and a single image would not
be able to capture this entire data contained in an actual specimen (Ceriaco et al. 2016; Rogers et al. 2017).
Conclusion
Our work shows that digital
images used for insect taxonomy can be edited to an extent which doesn’t alter
the image properties and thereby morphological characters altogether but,
enhances it enough so that it can be used in taxonomical research. These methods are quite easy to perform as
well. We also stress on the fact that a
poor image with heavy editing is no substitute for a properly taken one with
less editing or no editing.
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