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Corresponding author: Martijn Van Roie ( martijn.vanroie@uantwerpen.be ) Academic editor: Didier Vanden Spiegel
© 2017 Jan Mertens, Martijn Van Roie, Jonas Merckx, Wouter Dekoninck.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Mertens JEJ, Van Roie M, Merckx J, Dekoninck W (2017) The use of low cost compact cameras with focus stacking functionality in entomological digitization projects. ZooKeys 712: 141-154. https://doi.org/10.3897/zookeys.712.20505
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Digitization of specimen collections has become a key priority of many natural history museums. The camera systems built for this purpose are expensive, providing a barrier in institutes with limited funding, and therefore hampering progress. An assessment is made on whether a low cost compact camera with image stacking functionality can help expedite the digitization process in large museums or provide smaller institutes and amateur entomologists with the means to digitize their collections. Images of a professional setup were compared with the Olympus Stylus TG-4 Tough, a low-cost compact camera with internal focus stacking functions. Parameters considered include image quality, digitization speed, price, and ease-of-use. The compact camera’s image quality, although inferior to the professional setup, is exceptional considering its fourfold lower price point. Producing the image slices in the compact camera is a matter of seconds and when optimal image quality is less of a priority, the internal stacking function omits the need for dedicated stacking software altogether, further decreasing the cost and speeding up the process. In general, it is found that, aware of its limitations, this compact camera is capable of digitizing entomological collections with sufficient quality. As technology advances, more institutes and amateur entomologists will be able to easily and affordably catalogue their specimens.
Focus Stacking, Compact Camera, Canon-Cognysis, Mass Digitization, Entomology, Collections
Many museums rely on the help of volunteers for collection work (
Museums usually own a small number of digital imaging systems, constraining the digitization of collections, and can barely keep up with new additions to the collections. The professional setups typically require some level of training to use and have a high cost (€ 3.000 – € 30.000,
The rapid advancement in imaging technology and software over the past few years has resulted in high-quality, user-friendly and more affordable imaging systems (e.g., the focus stacking method currently used in the Royal Belgian Institute of Natural Sciences (
Comparison in price (minimum prices) and processing speed of the Canon-Cognisys setup with both TG-4’s stacking modes. 1aCanon EOS 600D with 60mm EF-S f/2.8 macro lens; 1bCanon EOS 600D with 65mm MP-E f/2.8 macro lens; 2off-camera flashes and platform; 3price for lifetime license of Helicon Focus Lite; 4post-processing time depends on processor type and speed among other factors; 5data from
Canon-Cognisys | TG-4 manual | TG-4 internal | ||
---|---|---|---|---|
Camera | € 8801a | € 15001b | € 350 | |
Stacking set-up | € 700 | N/A | ||
Stacking software cost2 | € 100 | € 100 | € 0 | |
Lightbox cost | € 1203 | € 25 | ||
Total cost | € 1800 | € 2420 | € 475 | € 375 |
#images in stack | Unlimited | 29 | 10 | |
Image resolution | 4.3 µm/pixel | 1.3 µm/pixel | 1.9 µm/pixel | |
Time to produce image | 5” per image in stack | 3” | 13”6 | |
Post-processing time4 | 17”5 | 28” |
The applicability of a compact camera was tested in view of a small digitization project of the genus Calligrapha (Coleoptera – Chrysomelidae) in the Royal Belgian Institute for Natural Sciences (
The Olympus Stylus TG-4 Tough (TG-4) was used in this test. Several compact cameras focusing on macro functionality are available on the market; however, they either lack internal focus stacking (e.g., for a comparison with the Nikon Coolpix AW130, see
The camera is a rugged, dust- (IPX6) and waterproof (IPX8) outdoor camera with an in-camera focus-stacking feature. This camera generally gets good reviews in terms of its macro capabilities (e.g.,
The camera’s capabilities were tested using five insect specimens varying in size and colour. Its image quality was compared with that of the professional setup, assessing image sharpness and level of detail and presence of stacking artefacts. In addition, distance to lens, zoom level and stacking method were altered.
Specimens from the genera Aplagiognathus (Coleoptera - Cerambycidae) and Elytrimitatrix (Coleoptera - Cerambycidae) were selected. The Aplagiognathus specimen was chosen for its larger size (length: 4.9 cm, width: 1.8 cm, height: 1.6 cm), uniform colour and microsculpture. The Elytrimitatrix specimen (length: 2.5 cm, width: 0.7 cm (2.3 cm including antennae), height: 0.5 cm) was chosen for its hairy abdomen, which often poses a problem when stacking (
Our own lightbox design was used, specifically made to be used with the compact camera. The body consists of a cylindrical plastic container with a hole on top that fits the lens of the camera. Inside, the top of the cylinder is lined with 59 12V, dimmable, white LED lights, covered by tracing paper to reduce light reflection on the specimens (Suppl. material
Manual stacking was initially performed using the free software package CombineZP (http://alan-hadley.software.informer.com). A recent review showed that this software package underperforms in comparison with commercial packages like Helicon Focus (http://www.heliconsoft.com/heliconsoft-products/helicon-focus/) and Zerene stacker (http://zerenesystems.com/cms/home), mostly when complex structures like hairs are involved (
To ascertain the compact camera’s performance and to find the optimal position of the specimens, firstly the two specimens of longhorn beetles (Aplagiognathus and Elytrimitatrix) were photographed. The camera’s two stacking methods, internal and manual stacking, were visually assessed and compared to macro-photographs of these specimens from the Canon-Cognisys setup. Next, the object-lens distance (11–5 cm, with 2 cm increments) and optical zoom (1–4 times) were altered to find an optimal set of parameters. Finally, pictures of Archips podana, Polistes dominula and Forficula auricularia (shot in manual stacking mode with specimens at an optimal distance from the lens) were visually assessed as well, to explore applicability in a wider taxonomic range.
A comparison of the two stacking settings (internal and manual stacking) with the professional setup can be seen in Figure
Comparison of the Elytrimitatrix digitized with the professional setup (A shot with the 60 mm macro lens and B with the Canon MP-E 65 mm lens), the compact camera’s manual focus stacking mode (C) and internal stacking mode (D). A depicts the whole specimen as would be shot for publication purposes. The red box indicates the section shown in B, C, D and the blue box indicates how the specimen was framed in these three images. Note that the stronger reflections in C, D are the result of a different lighting setup.
Assuming the handling time to position the specimen is similar in all situations, the time required to finish one stacked image differs more among methods (Table
To assess any noticeable reduction in sharpness when altering the optical zoom, sample pictures at four levels of magnification were taken. No so-called ‘sweet spot’ (optimal zoom range of a lens) at a certain zoom level could be observed (Figure
Visualization of the variation in image quality, level of detail and proportion of the specimen fitting the frame (insets) at different levels of optical magnification (1–4 times) and distance from the lens (11–5 cm). Every image, shot with the compact camera, is composed of 29 manually stacked images at the narrow setting and cropped to equal dimensions (approx. 1/24 of the original image). Quality and detail improve as lens distance decreases and/or the zoom increases at the cost of reduced depth of field and a smaller portion of the specimen fitting the image frame.
Comparison of image quality between the compact camera (A) and the professional setup (B) with the specimen occupying the same proportion of the frame. A detail is shown below. The compact camera was set up 5 cm from the specimen with the optical zoom at 1×, 29 images (narrow setting) were manually stacked. The professional setup outperforms the compact camera, producing a sharper image when specimens larger than a few centimetres are set to fill the frame optimally.
Figure
Images of different taxonomic groups, shot by the compact camera in manual mode (narrow setting). A large fruit-tree tortrix (Archips podana (Lepidoptera - Tortricidae)) B European paper wasp (Polistes dominula (Hymenoptera - Vespidae)), and C common earwig (Forficula auricularia (Dermaptera - Forficulidae)).
The internal stacking and the manual stacking mode of a compact camera were compared with a professional museum imaging setup. We found that in terms of picture detail and centre sharpness, the compact camera’s images are often comparable to the professional setup when it comes to image quality. However, pictures shot with the first, likely due to its limiting 10 (internal stacking mode) or 29 (manual stacking mode) images per stack and limited options defining the focal distance between each image (“wide”, “normal” and “narrow”), were more prone to local loss of focus (e.g., along the edges). The latter is especially clear when the object of interest spans the whole frame. The narrow setting results in marginally sharper images, barely noticeable in areas with more depth. However, due to the limited focus range, extremities (i.e., legs and antennae), and ‘deeper’ parts of the body fall out of focus. This can be alleviated by focusing exactly in the middle (i.e., mid-depth) of the specimen, for example more towards the head instead of the highest point of the abdomen. The normal setting usually solves this problem, broadening the focus range sufficiently to include the whole specimen. The professional setup is more versatile as its number of images in a stack can be adjusted, based on a predefined focus range and step size. Decreasing the step size results in a smoother transition from slice to slice and setting the focus range ensures the fore- and background to be out of focus. Therefore, the professional setup can provide a sharp image across the whole specimen, regardless of its shape or size.
The relatively small sensor size of the TG-4 (6.17 mm × 4.55 mm), when compared to any SLR camera (e.g., Canon APS-C: 22.3 mm × 14.9 mm), is unable to capture the amount of detail the professional setup can and, together with the limited number of images in a stack, can result in a less detailed image with parts of the frame being less sharp, especially when framing a large specimen (i.e., fully zoomed out and more distant from the lens). Nevertheless, the images shot by the compact camera retain key taxonomic features such as hairs and punctures. Additionally, the abovementioned stacking imperfections are often corrigible in the stacking software. This, however, requires the user to select manually which parts of one slice should be used in the final stacked image, increasing the processing time per stacked image.
When comparing the internal and manual stacking, it was found that a sharper image is achieved in manual stacking mode. This result is influenced by several factors, including the higher number of pictures in a manual stack (29 versus 10 in internal mode), the higher image resolution to 16MP (instead of 8MP) and the possibility to adjust focus range from narrow to wide. We should note, however, that the quality of manually stacked pictures also depends on the capabilities and limitations of the stacking software. Results varied when stacking the same batch of images in the freely available CombineZP software after which we opted to use the professional Helicon Focus software. Even though manual stacking is more time consuming (28 seconds per stack versus 13 seconds with internal stacking), most of this work can easily be batched in the stacking software and ran without user interaction using the Helicon pro license. The time spent transferring, organising, and labelling files onto the computer to prepare for Helicon’s stacking depends on the number of images and can easily add several minutes to the process. Another advantage of the stacking software, are the options to fine-tune several stacking algorithm parameters like smoothing and radius (http://www.heliconsoft.com/helicon-focus-main-parameters/) to improve the final image quality.
Apart from technical aspects, internally stacked pictures can easily be checked for incorrect focus on the camera’s LCD screen whereas errors in manually stacked pictures due to some parts of the specimen being not in focus are usually only discovered after processing. We would only recommend the internal stacking mode when no workstation and/or sufficient hard drive space are available (i.e., 29 image slices of one specimen can take up to 100Mb unstacked and 5Mb when stacked, whereas an automatically stacked image usually takes up below 2Mb).
The optical zoom did not substantially affect image quality. The feature that mattered most was the distance to the lens; the smaller the distance between the specimen and the lens, the more details could be discerned (e.g., punctuation, hairs). Nevertheless, there is a subtle functional difference between zoom versus distance to lens. Increasing the optical zoom slightly compresses the image stack, resulting in a smaller focus range. Zooming in is therefore practical when capturing details (e.g., microstructures and small setae) but less so when framing a specimen that requires more focus depth (e.g., a frontal view or legs stretching down far below the specimen’s body). Consequently, it is recommended to position such specimens closer to the lens instead of zooming in to profit from the larger focus range, the opposite is true for small specimens. Even though the focus compression effect is small, it is easy to take into account when positioning the specimen and might help retain more details in the stacked image. It could also prove to be helpful to adjust the focal step size, where a narrow step size often generates marginally better results, but could miss some parts of bigger specimens whereas a normal or wide setting wouldn’t.
One other drawback of using the compact camera tested in this study on larger specimens is the trade-off between detail and a full view of the specimen (Figure
In light of applicability to a wider taxonomic range than just Coleoptera, we tested the manual stacking mode to three other specimens: a European paper wasp (Polistes dominula (Hymenoptera - Vespidae)), a common earwig (Forficula auricularia (Dermaptera - Forficulidae)) and a large fruit-tree tortrix (Archips podana (Lepidoptera - Tortricidae)). In general, the resulting pictures are of good quality and detail. Some errors can remain, however, due to the limited focal step size adjustability, for example a slight tilt of the wing in Lepidoptera can cause certain parts to be out of focus. For large specimens or large-winged insects, this might pose an inconvenience. Note that these specimens surpassed the ‘ideal’ range of 1–2 cm. Additionally, the typical reduction of image sharpness towards the corners might influence the optimal positioning of a specific specimen. We recommend to always evaluate this beforehand.
When it comes to digitization of entomological collections, it seems that compact camera models such as the TG-4, used in this study, cannot out-compete professional imaging systems such as the Canon-Cognisys setup. This is in part due to the limited number of images in a stack and lower versatility when it comes to specimen dimensions. In situations where higher quality images are preferred (e.g., type material), specimens should be digitized with a professional, high quality setup. Nevertheless, compact camera models are a valuable addition to the professional setup for rapid specimen digitization. The ease of use and affordability could help reduce the digitization backlog of large museums or be the primary means to digitize specimens of personal collections or smaller institutes. This camera performs best for small specimens (around 1–2 cm) because they can be positioned closer to the lens without falling out of frame or reach the camera’s minimum focus distance. The manual stacking function, with 29 images, generates the best results, but has a significantly longer (post-)processing time. The latter can however be avoided by investing in a professional stacking software package with batching functionality. We do not recommend using the automatic stacking mode unless no workstation with stacking software or sufficient hard drive space is available. It generates a lower quality image; however, depending on the taxonomic group, it should still show key taxonomic features with sufficient detail to be useful to experts.
Trade-offs aside, budget compact cameras are constantly improved upon, including their macro capabilities and functions. The emergence of focus stacking features is an important step towards affordable professional-grade macroscopic images. Consequently, digitization of insect specimens has become affordable for most people and institutes. The internal stacking function could eliminate the cost of a dedicated stacking program and further costs (i.e., lightbox) are negligible. Together with a good volunteer program, a combination of a professional setup for type specimen digitization and compact cameras with focus stacking functionality could drastically speed up digitization efforts in an affordable way.
We greatly acknowledge Pol Limbourg for logistic support, Camille Locatelli for taking pictures with the museum setup, and Koen Martens for a first stage help with collection digitization. Staf Van Roie is acknowledged for his help and advice in constructing the light room. Alex Laking is acknowledged for a grammar check of the paper, and the reviewers are thanked for their valuable feedback.
Jan E.J. Mertens and Martijn Van Roie shared 1st authorship
Figure S1
Data type: PNG File (.png)
Explanation note: Lightbox setup, the camera rests on top of the cut-off bucket, its lens protruding though the hole in the middle. The specimen is usually shielded from direct light by a free-standing cylinder of tracing paper (not depicted). The LED strips on the inside are powered through a 12V adapter.
Figure S2
Data type: JPG File (.jpg)
Explanation note: Comparison of the narrow (C, F), normal (A, B, D, G) and wide (E, H) focal step size in two specimens of different ‘depth’ (A, C–E: Allochroma sp., 2 mm deep; B, E–H: Doryphora sp., 12 mm deep, measured from top of elytra to lowest tarsi). The narrow setting is marginally sharper in some areas; however, deeper parts of the specimen are not in focus. The wide setting produces artefacts around some of the edges, sometimes resulting in less sharp regions.