Applications of Computational 3D–Modeling in Organismal Biology

Laforsch, Christian; Imhof, Hannes K.; Sigl, Robert; Settles, Marcus; Heß, Martin; Wanninger, Andreas

doi:10.5772/31092

Cited by 21 publications

(22 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Non-destructive three-dimensional imaging techniques such as confocal laser scanning microscopy (cLSM), optical projection tomography (OPT), magnetic resonance imaging (MRI) and micro-computed tomography (micro-CT), allow for rapid creation of high-resolution morphological and anatomical data in three dimensions (Giribet 2010, Ziegler et al 2008, 2010, 2011a, for a detailed overview of the different techniques see e.g. Boistel et al 2011, Laforsch et al 2012). These techniques allow detailed virtual reconstructions of the morphology and anatomy of specimens and subsequent interactive manipulation (e.g.…”

Section: Introductionmentioning

confidence: 99%

Micro-computed tomography: Introducing new dimensions to taxonomy

Faulwetter¹,

Vasileiadou²,

Kouratoras³

et al. 2013

189

217

View full text Add to dashboard Cite

Continuous improvements in the resolution of three-dimensional imaging have led to an increased application of these techniques in conventional taxonomic research in recent years. Coupled with an ever increasing research effort in cybertaxonomy, three-dimensional imaging could give a boost to the development of virtual specimen collections, allowing rapid and simultaneous access to accurate virtual representations of type material. This paper explores the potential of micro-computed tomography (X-ray micro-tomography), a non-destructive three-dimensional imaging technique based on mapping X-ray attenuation in the scanned object, for supporting research in systematics and taxonomy. The subsequent use of these data as virtual type material, so-called “cybertypes”, and the creation of virtual collections lie at the core of this potential. Sample preparation, image acquisition, data processing and presentation of results are demonstrated using polychaetes (bristle worms), a representative taxon of macro-invertebrates, as a study object. Effects of the technique on the morphological, anatomical and molecular identity of the specimens are investigated. The paper evaluates the results and discusses the potential and the limitations of the technique for creating cybertypes. It also discusses the challenges that the community might face to establish virtual collections. Potential future applications of three-dimensional information in taxonomic research are outlined, including an outlook to new ways of producing, disseminating and publishing taxonomic information.

show abstract

Section: Introductionmentioning

confidence: 99%

Micro-computed tomography: Introducing new dimensions to taxonomy

Faulwetter¹,

Vasileiadou²,

Kouratoras³

et al. 2013

189

217

View full text Add to dashboard Cite

show abstract

“…As technological improvements have long been linked to scientific advances, 3D models of complex and irregular organisms provide us a new set of data to unveil not only geometric information (e.g. shape, form, volume) but also how these data change with time (Laforsch et al., ). Thus, our results on the mechanism that reduce evaporative water loss are not the ultimate end for these generated data.…”

Section: Discussionmentioning

confidence: 99%

Anuran 3D models reveal the relationship between surface area‐to‐volume ratio and climate

Amado

Pinto

Olalla‐Tárraga

2019

Journal of Biogeography

View full text Add to dashboard Cite

Aim The relationship size–environment has been continuously debated for ectotherms. Surface‐to‐volume ratios are recurrently suggested as the cause of body size responses to climate, but most inferences on organismal size clines stem from single linear measurements of body length. Here, we illustrate how new photogrammetric techniques can be applied to characterize amphibian morphologies with 3D models. Using the natterjack toad (Epidalea calamita) as model organism, we compared the performance of climatic models in accounting for body size (measured as snout‐to vent length, SVL) and body geometry (surface area‐to‐volume ratios) variation across macroclimatic gradients. Location Palaearctic. Taxon Epidalea calamita (former genus Bufo). Methods We used photogrammetry techniques to reconstruct 104 museum specimens of Epidalea calamita into 3D models and to collect geometric data (volume and surface area) to calculate surface area‐to‐volume ratios (SA:V). We then apply spatial and non‐spatial regression to examine the relationships between SA:V, SVL and a set of bioclimatic variables. Results In accordance with the water conservation hypothesis, SA:V decreased towards more arid environments, a pattern that remained consistent after accounting for spatial autocorrelation effects. Only mean annual temperature was significant correlated with SVL. The contrast between both sets of models indicates that more traditional body size metrics (SVL) and body geometry (SA:V) do not operate the same constraints. Main conclusions We show that the variation in SA:V can be explained by the geographical variation in aridity. Evaporative water loss in wet‐skinned ectotherms is highly dependent on the surface area of the skin exposed to the air. In contrast, SVL models detected that body length was more associated with mean annual temperature. This finding stresses the importance of selecting different metrics of body geometry and body size when examining variation across climatic gradients.

show abstract

“…However, the adoption of such media in taxonomy is still relatively scattered, and is mostly limited to MRI and Micro-computed Tomography (e.g. Mietchen et al 2008, Boistel et al 2011, Laforsch et al 2012, Faulwetter et al 2013). This may be due to the perception that sophisticated imaging requires special software, e-infrastructure and significant funding.…”

Section: Discussionmentioning

confidence: 99%

Rotational Scanning Electron Micrographs (rSEM): A novel and accessible tool to visualize and communicate complex morphology

Cheung¹,

Brunke²,

Akkari³

et al. 2013

View full text Add to dashboard Cite

An accessible workflow is presented to create interactive, rotational scanning electron micrographs (rSEM). These information-rich animations facilitate the study and communication of complex morphological structures exemplified here by male arthropod genitalia. Methods are outlined for the publication of rSEMs on the web or in journal articles as SWF files. Image components of rSEMs were archived in MorphBank to ensure future data access. rSEM represents a promising new addition to the toolkit of a new generation of digital taxonomy.

show abstract

Applications of Computational 3D–Modeling in Organismal Biology

Cited by 21 publications

References 63 publications

Micro-computed tomography: Introducing new dimensions to taxonomy

Micro-computed tomography: Introducing new dimensions to taxonomy

Anuran 3D models reveal the relationship between surface area‐to‐volume ratio and climate

Rotational Scanning Electron Micrographs (rSEM): A novel and accessible tool to visualize and communicate complex morphology

Contact Info

Product

Resources

About