Abstract
This article focuses on virtual advances to solve technical problems usually encountered by paleontologists, such as (i) the limited acquisition size of the computed tomography machines to acquire data on large structures, (ii) the use in the same study of biological objects acquired with different types of computed tomography, and therefore different resolutions, and (iii) matrix removal within the fossil (cranial cavities, intra-trabecular cavities, among others cavities). All these problems are very common problems in paleontology, and therefore, solving then is important to save effort and the time invested in data processing. We propose various solutions to remove such artefacts, based on new technical advance focused on improving and processing the images obtained from the X-ray computed tomography acquisition. Other aspects could be the use of filters to remove background noise from XCT data and measuring histograms to remove artefacts. Such artefacts are the result of recrystallizations or very dense materials within the samples, especially fossils due to the taphonomic fossilization process or derived from anthropogenic restoration of fossils. Accordingly, here, we provide a protocol to gradually acquire data on samples with size that exceed the size of the acquisition window of the X-ray tomography machine, joining the parts with enough accuracy and resolution, and we propose the use of the interpolation "bicubic" method. Moreover, using this method it is possible to use medical XCT data together with Xmicro-CT data, which opens new ways to use different tools to be able to rotate or move the acquired data within the image stack. Another advantage is the use of plugins for quantitative analysis, which is necessary to have data with isometric voxels, such as the BoneJ plugin of the software ImageJ. We also deal with the problem of eliminating the exogenous material that usually fills the internal cavities of fossils by means of using filters based on edge detection by gradient. Applying this method, it is possible to segment the non-bony matrix parts more quickly and efficiently. All of this is exemplified using five fossil skulls belonging to the cave bear group, an iconic fossil species from the Pleistocene of Eurasia.
Highlights
The advent of personal computers and digital technology in the twentieth century has allowed the emergence of new digital tools useful in paleontological research, including new software for image analysis and computational analysis (Jablonski and Shubin, 2015; du Plessis and Broeckhoven, 2019)
The Methods on X-ray computed tomography (XCT) Scan and Virtual Models generated and can be subject to different evolutionary studies using 3D geometric morphometrics (GMM) for ecomorphology (Drake, 2011), finite element analysis for biomechanics (Racicot, 2017; Tseng et al, 2017), or computational fluid dynamics to decipher the behavior of extinct animals in fluid environments (e.g., Rahman, 2017)
Our main objective is to provide new protocols of existing tools to solve the aforementioned problems, that is, (i) to eliminate artifacts typical of the use of XCT technology; (ii) to solve problems of data anisotropy, which is important when comparing different types of XCT data, i.e., from medical XCT or laboratory XCT with XμCT; (iii) to improve segmentation and to improve the virtually cleaning of those materials that usually encompass or fill the internal structures of fossils; (iv) to restore and replace lacking parts of fossils in order to provide an accurate anatomical reconstruction; and (v) to solve errors accumulated in previous processes by processing the mesh and quantifying the topological deviation resulting from previous restorations
Summary
The advent of personal computers and digital technology in the twentieth century has allowed the emergence of new digital tools useful in paleontological research, including new software for image analysis and computational analysis (Jablonski and Shubin, 2015; du Plessis and Broeckhoven, 2019). In the case of paleontology, this “digital revolution” has substantially changed the way of analyzing the scientific material, generating new fields of research at different levels of analysis that were previously inaccessible (Racicot, 2017) This is the case of histological studies in fossils with non-invasive techniques (i.e., virtual paleohistology; e.g., Sanchez et al, 2012), virtual reconstructions of distorted fossil specimens with lacking parts (i.e., retrodeformation techniques; e.g., Tallman et al, 2014), development of powerful biomechanical models (i.e., finite element analysis; e.g., Figueirido et al, 2014, 2018; Tseng et al, 2017; Pérez-Ramos et al, 2020), or the study of internal structures, non-accessible without using invasive techniques such as brain endocasts (i.e., paleoneurology; e.g., Cuff et al, 2016) or paranasal sinuses and turbinates (i.e., functional anatomy of internal structures; e.g., Curtis and Van Valkenburgh, 2014; Van Valkenburgh et al, 2014; Matthews and du Plessis, 2016). All these techniques undoubtedly lead to new avenues for future research in the paleobiology of extinct organisms
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