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The results of the different stacking methods in Helicon Focus: each stacking option is provided with a detail of a hairy leg and a part of the head with hairs. A, B result of Method A (average) C, D result of Method B (depth) E, F result of Method C (pyramid).
Source publication
In this manuscript we present a focus stacking system, composed of commercial photographic equipment. The system is inexpensive compared to high-end commercial focus stacking solutions. We tested this system and compared the results with several different software packages (CombineZP, Auto-Montage, Helicon Focus and Zerene Stacker). We tested our f...
Contexts in source publication
Context 1
... the three methods available, the 'Pyramid' method (Method C, Figures 4E, F), as suggested by the guidelines of Helicon Focus, proved the most satisfactory. There are almost no halos present on the image and it has a clean look, but the brightness and the contrast is changed by the software. ...
Context 2
... another background this may work, but here it further distorts the image rather than accentuating it. The 'Depth' method (Method B, Figures 4C, D) is not suited for these types of specimens as the hairs produce halos all over the specimen. However, this can be controlled by adjusting the radius when choosing the depth method. ...
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Citations
... Automatic Registration requires no further input aside from the two images. Automatic registration works well for many tasks with similar images taken shortly after each other from the same position and with the same camera, e.g., panorama stitching [204], HDRI [205], or focus stacking [206]. The challenges in rephotography (Section 6) hinder all standard automatic registration algorithms. ...
Repeat photography, the process of locating the camera position of an old photo and taking a new photo from this position, is utilized to protect our natural heritage, by measuring landscape changes between old and new image, and to conserve and recover our architectural and archaeological heritage, by observing changes between images taken before, during, and after conservation efforts or destructive events. Most importantly, repeat photography—in short, rephotography—is connecting us to our heritage on all levels from personal to global: while rephotographing, we connect with the old image and its creator and—when viewing and comparing the old image and the rephotograph—we connect with the tangible, intangible, and natural heritage shown in the images by observing changes and continuities. In this paper, we review publications and applications employing rephotography. We discuss the organization, retrieval, and presentation of rephotographic compilations, their generation by different image registration techniques, and their conservation as rephotographic heritage. Further, we describe challenges in rephotography, discuss how they differ from standard challenges in photography, computer vision, and image registration and present both analog and digital solutions and tools used in practice by rephotographers to address said challenges.
... While voucher specimens remain the gold standard format for archiving biodiversity and conferring repeatability in scientific studies, digital products such as two-dimensional images and computed tomography (CT) media serve as extensions of physical collections and add value and utility to preserved specimens (Beaman and Cellinese 2012;Webster 2017;Hedrick et al. 2020;Lendemer et al. 2020;Hilton et al. 2021). Such digital proxies also play a vital role in the long-term preservation of primary resources, at times circumventing the need to loan, handle, or dissect specimens, thereby reducing risks to physical collections (Blagoderov et al. 2012;Brecko et al. 2014;Page et al. 2015;Lendemer et al. 2020). ...
... helicon-focus/) and Zerene Stacker (http://www.zerenesystems.com/cms/stacker), which have been found to perform equally well (Brecko et al. 2014). These programs offer various methods for combining image stacks, built-in retouching tools, batch workflows, image naming and export options, and plugin integrations with Adobe Lightroom. ...
Fluid-preserved reptile and amphibian specimens are challenging to photograph with traditional methods due to their complex three-dimensional forms and reflective surfaces when removed from solution. An effective approach to counteract these issues involves combining focus stack photography with the use of a photo immersion tank. Imaging specimens beneath a layer of preservative fluid eliminates glare and risk of specimen desiccation, while focus stacking produces sharp detail through merging multiple photographs taken at successive focal steps to create a composite image with an extended depth of field. This paper describes the wet imaging components and focus stack photography workflow developed while conducting a large-scale digitization project for targeted reptile and amphibian specimens housed in the University of Colorado Museum of Natural History Herpetology Collection. This methodology can be implemented in other collections settings and adapted for use with fluid-preserved specimen types across the Tree of Life to generate high-quality, taxonomically informative images for use in documenting biodiversity, remote examination of fine traits, inclusion in publications, and educational applications.
... For example, Mertens et al. have reported a low-cost camera for entomological digitalization projects [19]. Brecko et al. have also demonstrated a semiautomatic instrument setting and compared the relative performance of several different software on stacked image quality and performance [20]. ...
... These features also have overcome some limitations faced by other previously published low-cost setups, such as the limited number of images in a stack and lower versatility when it comes to specimen dimensions encountered by the prior setup demonstrated by Mertens et al. with compact cameras with focus stacking functionality [19]. Furthermore, since the current method is a video-based method, it enables users to obtain more images in a shorter time compared to the semi-automatic low-budget approach provided by Brecko et al. [20]. In addition, although other methods can also do an image stacking of living subjects, they require high-end cameras and lenses with built-in focus bracketing functions (e.g., Olympus EM1 Mark 2). ...
Image stacking is a crucial method for micro or macro photography. It captures images at different focal planes and then merges them into a single, all-in-focus image with extended focus. This method has been extensively used for digital documentation by scientists working at museums or research institutions. However, the traditional image stacking method relies on expensive instruments to conduct precise image stacking using a computer-based stepper motor controller. In this study, we reported how to conduct image focus extensions with comparable quality to those done by a motorized stepper using a cost-effective instrument setting and an efficient manual stacking method. This method provides a shorter operation time and capability to capture images of living objects and high flexibility in obtaining the images of objects from cm to mm scale. However, it also has some
limitations, including the inability to control aperture and exposure time, relatively short working distance at high magnification, requires additional steps to convert the video into images, and heavily relies on the user’s manual observation prior to a video recording. Nevertheless, the authors believe that the current method can be applied as an alternative method to conduct image stacking. The development of such an instrument and method offers a promising avenue for scientists to perform
image stacking with greater flexibility and speed in macro photography.
... Se puede llevar a cabo mediante dos métodos bastante similares: o bien desplazando la cámara unas micras o bien moviendo la anilla de enfoque y dejando la cámara fija. El objetivo, en ambos casos, es ir tomando fotografías donde la zona del objeto que aparece enfocada, según la profundidad de campo definida por el diafragma y aumento seleccionados, se vaya desplazando de atrás hacia adelante hasta registrar correctamente todo el espécimen (Brecko et al., 2014). ...
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... Another technique that is widely used in microphotography is focus stacking. 15 This digital technology is designed to achieve a greater depth of field (DOF) by blending multiple images. Each stacked shot is focused on a different depth, so the combined DOF image is larger than any of the individual source images. ...
... Last but not least, while the focus of this communication is largely on micro-CT, some of the many other new techniques that are being tested, used and improved will be highlighted (see e.g. Brecko & Mathys, 2020;Brecko et al., 2014Brecko et al., , 2016Brecko et al., , 2018Mathys et al., 2013Mathys et al., , 2019 for some examples). Interested in our work, expertise, techniques, equipment, or scans-ondemand? ...
Proceedings of the 7th International Geologica Belgica Congress: 15-17 September 2021 – Africamuseum Tervuren (Belgium) - Geosciences made in Belgium.
The Royal Museum for Central Africa was pleased to welcome the 7th international
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A total of 12 sessions were identified with 188 abstracts covering various disciplines
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different countries. There were 1 Medal presentation (Van den Broek Medal 2021),
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There were a large proportion of young scientists, and for several of them this was
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... However, examining this phenomenon in different acquisition scenarios can be crucial in a massive digitisation project for meeting the expected results. While this problem has been solved for a few objects adopting the focus stacking [23][24][25][26] or shape from focus [27] techniques, these solutions are impractical when digitisation includes numerous artefacts. While the focus stacking approach requires acquiring images with shallow DoF from different focusing distances to create a new image with a longer DoF, the shape from focus technique generates sharper images from a multi-focus image sequence based on a local variance criterion. ...
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... It should be noted that while both cameras we used had full-frame sensors, high-quality images can be produced using crop sensor cameras and lenses. A smaller sensor size trades off some degree of dynamic range and resolution, but crop sensor cameras have shown to be effective in specimen digitisation, in addition to being generally cheaper and more portable (Brecko et al., 2014;Brecko & Mathys, 2020). We used Lightroom CC 2015.14 (Adobe Inc., USA) to process images for white balance correction and quality control. ...
... We observe a transition to high resolution light photographic images, a positive trend, given the recent push to digitize collections. Although drawings certainly have value as interpretive images, high quality photographs of actual specimens (e.g., holotypes) are potentially data rich and in some cases may abrogate the need for borrowing material from collections [34]. ...
Planetary extinction of biodiversity underscores the need for taxonomy. Here, we scrutinize spider taxonomy over the last decade (2008–2018), compiling 2083 published accounts of newly described species. We evaluated what type of data were used to delineate species, whether data were made freely available, whether an explicit species hypothesis was stated, what types of media were used, the sample sizes, and the degree to which species constructs were integrative. The findings we report reveal that taxonomy remains largely descriptive, not integrative, and provides no explicit conceptual framework. Less than 4% of accounts explicitly stated a species concept and over one-third of all new species described were based on 1–2 specimens or only one sex. Only ~5% of studies made data freely available, and only ~14% of all newly described species employed more than one line of evidence, with molecular data used in ~6% of the studies. These same trends have been discovered in other animal groups, and therefore we find it logical that taxonomists face an uphill challenge when justifying the scientific rigor of their field and securing the needed resources. To move taxonomy forward, we make recommendations that, if implemented, will enhance its rigor, repeatability, and scientific standards.
