A rapid and cost-effective pipeline for digitization of museum specimens with 3D photogrammetry.
TL;DR: This work introduces an efficient and cost-effective pipeline for 3D photogrammetry to capture the external appearance of natural history specimens and other museum objects and shows that digital bill measurements are comparable to hand-taken measurements.
Abstract: Natural history collections are yielding more information as digitization brings specimen data to researchers, connects specimens across museums, and as new technologies allow for more large-scale data collection. Therefore, a key goal in specimen digitization is developing methods that both increase access and allow for the highest yield of phenomic data. 3D digitization is increasingly popular because it has the potential to meet both aspects of that key goal. However, current methods overlook or do not prioritize some of the most sought-after phenotypic traits, those involving the external appearance of specimens, especially color. Here, we introduce an efficient and cost-effective pipeline for 3D photogrammetry to capture the external appearance of natural history specimens and other museum objects. 3D photogrammetry aligns and compares sets of dozens, hundreds, or even thousands of photos to create 3D models. The hardware set-up requires little physical space and around $3,000 in initial investment, while the software pipeline requires $1,400/year for proprietary software subscriptions (with open-source alternatives). The creation of each 3D model takes 1-2 hours/specimen and much of the software pipeline is automated with minimal supervision required, including the onerous step of mesh processing. We showcase the method by creating 3D models for most of the type specimens in the Moore Laboratory of Zoology bird collection and show that digital bill measurements are comparable to hand-taken measurements. Color data, while not included as part of this pipeline, is easily extractable from the models and one of the most promising areas of data collection. Future advances can adapt the method for ultraviolet reflectance capture and increased efficiency and model quality. Combined with genomic data, phenomic data from 3D models including photogrammetry will open new doors to understanding organismal evolution.
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TL;DR: There is a rich history of detailed study on plumage patterns, which is reviewed and synthesize in this manuscript as mentioned in this paper, and an expanding toolbox of new methods that characterize and quantify the size, shape, and distribution of plumage patches.
Abstract: Birds exhibit remarkable variation in plumage patterns, both within individual feathers and among plumage patches. Differences in the size, shape, and location of pigments and structural colors comprise important visual signals involved in mate choice, social signaling, camouflage, and many other functions. While ornithologists have studied plumage patterns for centuries, recent technological advances in digital image acquisition and processing have transformed pattern quantification methods, enabling comprehensive, detailed datasets of pattern phenotypes that were heretofore inaccessible. In this review, we synthesize recent and classic studies of plumage patterns at different evolutionary and organismal scales and discuss the various roles that plumage patterns play in avian biology. We dissect the role of plumage patches as signals within and among species. We also consider the evolutionary history of plumage patterns, including phylogenetic comparative studies and evolutionary developmental research of the genetic architecture underlying plumage patterns. We also survey an expanding toolbox of new methods that characterize and quantify the size, shape, and distribution of plumage patches. Finally, we provide a worked example to illustrate a potential workflow with dorsal plumage patterns among subspecies of the Horned Lark (Eremophila alpestris) in western North America. Studies of plumage patterning and coloration have played a prominent role in ornithology thus far, and recent methodological and conceptual advances have opened new avenues of research on the ecological functions and evolutionary origins of plumage patterns in birds.LAY SUMMARYBirds have many different plumage patterns that arise from coloration motifs within feathers as well as differences in color among body regions.Plumage patterns play various roles in bird biology. They are involved in mate choice and territoriality, social interactions, camouflage from predators, and many other functions.There is a rich history of detailed study on plumage patterns, which we review and synthesize in this manuscript.Recent advances in photography and image processing algorithms have opened new avenues of research on plumage patterns. These open-source methods enable efficient, repeatable, and scalable analytical pipelines.We illustrate one possible pipeline with a worked example of geographic variation in dorsal plumage patterns among populations of Horned Lark (Eremophila alpestris) in the western United States.Looking ahead, enhanced capacity and scalability for digital photography analyses will reveal new discoveries regarding the ecology and evolution of avian plumage patterns.
18 citations
TL;DR: In this paper, the authors analyzed the changes in the position of Hiorthhamn shoreline (Svalbard), which is affecting coastal cultural heritage sites, for a period of 93 years (1927-2020).
Abstract: Strong cultural heritage management relies on a thorough evaluation of the threats faced by heritage sites, both in the present and in the future. In this study, we analysed the changes in the position of Hiorthhamn shoreline (Svalbard), which is affecting coastal cultural heritage sites, for a period of 93 years (1927–2020). Shoreline changes were mapped by using maps, ortophotos, drone images, terrestrial laser scanning (TLS), and topographic surveys. Also, TLS was used to 3D document the endangered coastal cultural heritage sites. Detailed sedimentological and morphological mapping was made in the field and from the newly acquired drone images in order to understand shoreline-landscape interaction and to depict changes occurring from 2019 to 2020. Short-term (2019–2020) and long-term (1927–2020) shoreline erosion/accretion was made with the help of the Digital Shoreline Analysis System (DSAS) and prompted a subdivision of three sectors, based on change pattern. Compared to a previous long-term analysis (1927–2019), this year’s average erosion rate analysis (expressed by the EPR parameter) for the 93-year period is −0.14 m/yr. This shift in mean development is due to a newly formed spit-bar in Sector 2. Referring strictly to Sector 1, where the protected cultural heritage objects are located, the erosion rate increased from the previous analysis of –0.76 m/yr to −0.77 m/yr. The shoreline forecast analysis highlights that half of the protected cultural heritage objects will likely disappear over the next decade and almost all the cultural heritage objects analysed in this study will disappear in roughly two decades. This shows the great danger the Arctic’s cultural heritage sites is in if no mitigation measures are undertaken by the local authorities.
14 citations
TL;DR: A comprehensive overview on the use of digital 3D technologies in the humanities with regards to scenarios, user communities, and epistemic challenges; technologies, UX design, and workflows; and framework conditions as legislation, infrastructures, and teaching programs is provided.
Abstract: Digital 3D modelling and visualization technologies have been widely applied to support research in the humanities since the 1980s. Since technological backgrounds, project opportunities, and methodological considerations for application are widely discussed in the literature, one of the next tasks is to validate these techniques within a wider scientific community and establish them in the culture of academic disciplines. This article resulted from a postdoctoral thesis and is intended to provide a comprehensive overview on the use of digital 3D technologies in the humanities with regards to (1) scenarios, user communities, and epistemic challenges; (2) technologies, UX design, and workflows; and (3) framework conditions as legislation, infrastructures, and teaching programs. Although the results are of relevance for 3D modelling in all humanities disciplines, the focus of our studies is on modelling of past architectural and cultural landscape objects via interpretative 3D reconstruction methods.
14 citations
04 Aug 2021
TL;DR: Describing a substantial proportion of the world’s species could be made much easier by the 3D digitization of collections, which would facilitate the dissemination of taxonomic information locked up in natural history museums.
Abstract: Describing a substantial proportion of the world’s species could be made much easier by the 3D digitization of collections, which would facilitate the dissemination of taxonomic information locked up in natural history museums. Three-dimensional imaging captures many characters and allows a lot of versatility in the way that morphological data is displayed and used (Wheeler et al. 2012; Faulwetter et al. 2013). Moreover, the loss and damage of valuable specimens, many of which are very fragile, can be reduced as a result of the use and sharing of 3D model substitutes among researchers. This can also lead to a reduction in the handling and transportation expenses of many specimens.
11 citations
Cites methods from "A rapid and cost-effective pipeline..."
...The cost of generating 3D models is cheapening due to advances in imaging technology, including new photogrammetric software (Medina et al. 2020; Plum & Labonte 2021)....
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References
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01 Jan 2004
TL;DR: ImageJ is an open source Java-written program that is used for many imaging applications, including those that that span the gamut from skin analysis to neuroscience, and can read most of the widely used and significant formats used in biomedical images.
Abstract: Wayne Rasband of NIH has created ImageJ, an open source Java-written program that is now at version 1.31 and is used for many imaging applications, including those that that span the gamut from skin analysis to neuroscience. ImageJ is in the public domain and runs on any operating system (OS). ImageJ is easy to use and can do many imaging manipulations. A very large and knowledgeable group makes up the user community for ImageJ. Topics covered are imaging abilities; cross platform; image formats support as of June 2004; extensions, including macros and plug-ins; and imaging library. NIH reports tens of thousands of downloads at a rate of about 24,000 per month currently. ImageJ can read most of the widely used and significant formats used in biomedical images. Manipulations supported are read/write of image files and operations on separate pixels, image regions, entire images, and volumes (stacks in ImageJ). Basic operations supported include convolution, edge detection, Fourier transform, histogram and particle analyses, editing and color manipulation, and more advanced operations, as well as visualization. For assistance in using ImageJ, users e-mail each other, and the user base is highly knowledgeable and will answer requests on the mailing list. A thorough manual with many examples and illustrations has been written by Tony Collins of the Wright Cell Imaging Facility at Toronto Western Research Institute and is available, along with other listed resources, via the Web.
12,060 citations
"A rapid and cost-effective pipeline..." refers methods in this paper
...While we did not specifically integrate color analysis into the pipeline, several open-source programs (like ImageJ; [50]) allow for detailed color analysis from flattened images created from 3D models (Fig 4)....
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TL;DR: The Structure-from-Motion (SfM) method as mentioned in this paper solves the camera pose and scene geometry simultaneously and automatically, using a highly redundant bundle adjustment based on matching features in multiple overlapping, offset images.
2,901 citations
"A rapid and cost-effective pipeline..." refers background in this paper
...First applied to landscapes and geological features [20, 21], 3D photogrammetry then moved to archaeology, paleontology, and cultural heritage sites [22–24], and eventually was improved to capture smaller and smaller objects [25, 26]....
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TL;DR: It is found that birds have undergone a strong increase in diversification rate from about 50 million years ago to the near present, with a number of significant rate increases, both within songbirds and within other young and mostly temperate radiations including the waterfowl, gulls and woodpeckers.
Abstract: Current global patterns of biodiversity result from processes that operate over both space and time and thus require an integrated macroecological and macroevolutionary perspective. Molecular time trees have advanced our understanding of the tempo and mode of diversification and have identified remarkable adaptive radiations across the tree of life. However, incomplete joint phylogenetic and geographic sampling has limited broad-scale inference. Thus, the relative prevalence of rapid radiations and the importance of their geographic settings in shaping global biodiversity patterns remain unclear. Here we present, analyse and map the first complete dated phylogeny of all 9,993 extant species of birds, a widely studied group showing many unique adaptations. We find that birds have undergone a strong increase in diversification rate from about 50 million years ago to the near present. This acceleration is due to a number of significant rate increases, both within songbirds and within other young and mostly temperate radiations including the waterfowl, gulls and woodpeckers. Importantly, species characterized with very high past diversification rates are interspersed throughout the avian tree and across geographic space. Geographically, the major differences in diversification rates are hemispheric rather than latitudinal, with bird assemblages in Asia, North America and southern South America containing a disproportionate number of species from recent rapid radiations. The contribution of rapidly radiating lineages to both temporal diversification dynamics and spatial distributions of species diversity illustrates the benefits of an inclusive geographical and taxonomical perspective. Overall, whereas constituent clades may exhibit slowdowns, the adaptive zone into which modern birds have diversified since the Cretaceous may still offer opportunities for diversification.
2,660 citations
"A rapid and cost-effective pipeline..." refers background in this paper
...Combined with large-scale genomic data [53, 54] and complete phylogenies for various organismal groups [55, 56], color data from 3D digital models will help elucidate links between genotype and phenotype....
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17 Jun 2006
TL;DR: This paper first survey multi-view stereo algorithms and compare them qualitatively using a taxonomy that differentiates their key properties, then describes the process for acquiring and calibrating multiview image datasets with high-accuracy ground truth and introduces the evaluation methodology.
Abstract: This paper presents a quantitative comparison of several multi-view stereo reconstruction algorithms. Until now, the lack of suitable calibrated multi-view image datasets with known ground truth (3D shape models) has prevented such direct comparisons. In this paper, we first survey multi-view stereo algorithms and compare them qualitatively using a taxonomy that differentiates their key properties. We then describe our process for acquiring and calibrating multiview image datasets with high-accuracy ground truth and introduce our evaluation methodology. Finally, we present the results of our quantitative comparison of state-of-the-art multi-view stereo reconstruction algorithms on six benchmark datasets. The datasets, evaluation details, and instructions for submitting new models are available online at http://vision.middlebury.edu/mview.
2,556 citations
"A rapid and cost-effective pipeline..." refers background in this paper
..., ‘Structure from Motion’) involves photographing an object from multiple angles, then using software that aligns common landmarks between the photographs to reconstruct a 3D model from sets of dozens, hundreds, or even thousands of photos [19]....
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University of California, Santa Cruz1, National Institutes of Health2, Broad Institute3, University of Los Andes4, University of Guelph5, University of Nottingham6, University of California, Berkeley7, Pennsylvania State University8, Royal Ontario Museum9, Texas A&M University10, Louisiana State University11, Agency for Science, Technology and Research12, University of Kansas13, University of Montana14, American Museum of Natural History15, Oregon State University16, Villanova University17, University of Porto18, Smithsonian Institution19, Oswaldo Cruz Foundation20, Okinawa Institute of Science and Technology21, University of Sheffield22, Harvard University23, Swedish Museum of Natural History24, University of Copenhagen25, Novosibirsk State University26, Australian National University27, Max Planck Society28, Field Museum of Natural History29, Commonwealth Scientific and Industrial Research Organisation30, Science Applications International Corporation31, Stanford University32, University of Illinois at Urbana–Champaign33, George Washington University34, Global Viral35, University of Bedfordshire36, Federal University of Rio de Janeiro37, University of California, Davis38, University of California, Riverside39, Museum Victoria40, University College Dublin41, Monterey Bay Aquarium Research Institute42, Washington University in St. Louis43, University of California, Los Angeles44, Kunming Institute of Zoology45
TL;DR: A precipitous drop in costs and increase in sequencing efficiency is anticipated, with concomitant development of improved annotation technology, and it is proposed to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future.
Abstract: American Genetic Association, Gordon and Betty Moore Foundation, NHGRI Intramural Sequencing Center, and UCSC Alumni Association to cost of the Genome 10K workshop; Howard Hughes Medical Institute to D. H.; Gordon and Betty Moore Foundation to S. C. S.; A
545 citations