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1. The Walking Dead: Status Report, Data Workflow and Best Practices of the oVert Thematic Collections Network

   https://doi.org/10.3897/biss.2.26078  

   Watkins-Colwell, Gregory ; Love, Kevin ; Randall, Zachary ; Boyer, Doug ; Winchester, Julie ; Stanley, Edward ; Blackburn, David ( June 2018 , Biodiversity Information Science and Standards)

   In 2017 NSF funded “oVert (openVertebrate): Open Exploration of Vertebrate Diversity in 3D,” which is the first Thematic Collections Network devoted entirely to vertebrate morphological specimens. The primary goal of oVert is to generate and serve high-resolution digital three-dimensional data for internal anatomy across vertebrate diversity. oVert will CT-scan >20,000 fluid-preserved specimens representing >80% of the living genera of vertebrates, providing broad coverage for exploration and research on all major groups of vertebrates. Contrast-enhanced scans will be generated to reveal soft tissues and organs for a majority of the living vertebrate families. This collection of digital imagery and three-dimensional volumes will be open for exploration, download, and use. These new media will provide unprecedented global access to valuable morphological data of specimens in US collections.oVert is developing best practices and guidelines for high-throughput CT-scanning, including efficient workflows, preferred resolutions, and archival formats that optimize the variety of downstream applications. Using the Integrated Digitized Biocollections (iDigBio) API, we have developed a workflow where people uploading media files to MorphoSource can search for and import metadata for specimens directly from iDigBio. Via a Rich Site Summary (RSS) feed from MorphoSource, Audubon Core data describing media files for a given scientific collection can be retrieved and integrated into institutional IPT and databases. Such data migration of large files requires attention to detail and the development of data workflows that ensure correct specimen mapping at all steps. The RSS feed from MorphoSource will also consolidate usage information for media files from specimens in each scientific collection for reporting. Additional goals of the project are to provide information vital to the creation of collection best practices for imaging permissions/copyright. A status report and update on best practices will be presented. 

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2. Manufacturing and Characterization of Hybrid Bulk Voxelated Biomaterials Printed by Digital Anatomy 3D Printing

   https://doi.org/10.3390/polym13010123  

   Heo, Hyeonu ; Jin, Yuqi ; Yang, David ; Wier, Christopher ; Minard, Aaron ; Dahotre, Narendra B. ; Neogi, Arup ( January 2021 , Polymers)

   null (Ed.)

   The advent of 3D digital printers has led to the evolution of realistic anatomical organ shaped structures that are being currently used as experimental models for rehearsing and preparing complex surgical procedures by clinicians. However, the actual material properties are still far from being ideal, which necessitates the need to develop new materials and processing techniques for the next generation of 3D printers optimized for clinical applications. Recently, the voxelated soft matter technique has been introduced to provide a much broader range of materials and a profile much more like the actual organ that can be designed and fabricated voxel by voxel with high precision. For the practical applications of 3D voxelated materials, it is crucial to develop the novel high precision material manufacturing and characterization technique to control the mechanical properties that can be difficult using the conventional methods due to the complexity and the size of the combination of materials. Here we propose the non-destructive ultrasound effective density and bulk modulus imaging to evaluate 3D voxelated materials printed by J750 Digital Anatomy 3D Printer of Stratasys. Our method provides the design map of voxelated materials and substantially broadens the applications of 3D digital printing in the clinical research area. 

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3. Constrained one‐step material decomposition reconstruction of head CT data from a silicon photon‐counting prototype

   https://doi.org/10.1002/mp.16649  

   Schmidt, Taly Gilat ; Sidky, Emil Y. ; Pan, Xiaochuan ; Barber, Rina Foygel ; Grönberg, Fredrik ; Sjölin, Martin ; Danielsson, Mats ( July 2023 , Medical Physics)

   Spectral CT material decomposition provides quantitative information but is challenged by the instability of the inversion into basis materials. We have previously proposed the constrained One‐Step Spectral CT Image Reconstruction (cOSSCIR) algorithm to stabilize the material decomposition inversion by directly estimating basis material images from spectral CT data. cOSSCIR was previously investigated on phantom data.

   This study investigates the performance of cOSSCIR using head CT datasets acquired on a clinical photon‐counting CT (PCCT) prototype. This is the first investigation of cOSSCIR for large‐scale, anatomically complex, clinical PCCT data. The cOSSCIR decomposition is preceded by a spectrum estimation and nonlinear counts correction calibration step to address nonideal detector effects.

   Head CT data were acquired on an early prototype clinical PCCT system using an edge‐on silicon detector with eight energy bins. Calibration data of a step wedge phantom were also acquired and used to train a spectral model to account for the source spectrum and detector spectral response, and also to train a nonlinear counts correction model to account for pulse pileup effects. The cOSSCIR algorithm optimized the bone and adipose basis images directly from the photon counts data, while placing a grouped total variation (TV) constraint on the basis images. For comparison, basis images were also reconstructed by a two‐step projection‐domain approach of Maximum Likelihood Estimation (MLE) for decomposing basis sinograms, followed by filtered backprojection (MLE + FBP) or a TV minimization algorithm (MLE + TV_min) to reconstruct basis images. We hypothesize that the cOSSCIR approach will provide a more stable inversion into basis images compared to two‐step approaches. To investigate this hypothesis, the noise standard deviation in bone and soft‐tissue regions of interest (ROIs) in the reconstructed images were compared between cOSSCIR and the two‐step methods for a range of regularization constraint settings.

   cOSSCIR reduced the noise standard deviation in the basis images by a factor of two to six compared to that of MLE + TV_min, when both algorithms were constrained to produce images with the same TV. The cOSSCIR images demonstrated qualitatively improved spatial resolution and depiction of fine anatomical detail. The MLE + TV_minalgorithm resulted in lower noise standard deviation than cOSSCIR for the virtual monoenergetic images (VMIs) at higher energy levels and constraint settings, while the cOSSCIR VMIs resulted in lower noise standard deviation at lower energy levels and overall higher qualitative spatial resolution. There were no statistically significant differences in the mean values within the bone region of images reconstructed by the studied algorithms. There were statistically significant differences in the mean values within the soft‐tissue region of the reconstructed images, with cOSSCIR producing mean values closer to the expected values.

   The cOSSCIR algorithm, combined with our previously proposed spectral model estimation and nonlinear counts correction method, successfully estimated bone and adipose basis images from high resolution, large‐scale patient data from a clinical PCCT prototype. The cOSSCIR basis images were able to depict fine anatomical details with a factor of two to six reduction in noise standard deviation compared to that of the MLE + TV_mintwo‐step approach.

    

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4. Computed Microtomography (Micro-CT) in the Anatomical Study and Identification of Solenogastres (Mollusca)

   https://doi.org/10.3389/fmars.2021.760194  

   Martínez-Sanjuán, J. ( January 2022 , Frontiers in marine science)

   Solenogastres are vermiform marine molluscs characterised by an aculiferous mantle, a longitudinal ventral pedal groove and a terminal or subterminal pallial cavity. Their classification is based in part on the type of mantle sclerites, but identification to even the family level generally requires the study of internal anatomical characters. Taxonomically important internal characters include those related to radular structure, the type of ventrolateral glandular organs of the pharynx and the reproductive system, among others. In order to study their internal anatomical organisation, according to the classical reconstruction method, serial histological sections of specimens are made, from which the 2D internal anatomy of the specimen can be reconstructed manually. However, this is a time-consuming technique that results in destruction of the specimen. Computed microtomography or micro-CT is a non-destructive technique based on the measurement of the attenuation of X-rays as they pass through a specimen. Micro-CT is faster than histology for studying internal anatomy and it is non-destructive, meaning that specimens may be used for e.g., DNA extraction or retained as intact vouchers. In this paper, the utility of micro-CT for studying taxonomically important internal anatomical structures was assessed. Results of the 3D anatomical study of the soft parts of four specimens of three species using micro-CT are presented: Proneomenia sluiteri Hubrecht, 1880, Dorymenia menchuescribanae García-Álvarez et al., 2000 and Anamenia gorgonophila Kowalevsky, 1880. Micro-CT enabled detailed study of most taxonomically important anatomical characters, precise measurements of structures, and observation of the relative position of organs from a variety of angles. However, it was not possible to observe the radula and some details of the ventral foregut organs could not be discerned. Despite these limitations, results of this study highlight micro-CT as a valuable tool to compliment histology in the study of solenogaster anatomy and in non-destructively identifying animals to the family and even genus-level. 

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5. 3D Digitization in Functional Morphology: Where is the Point of Diminishing Returns?

   https://doi.org/10.1093/icb/icz101  

   Santana, Sharlene E ; Arbour, Jessica H ; Curtis, Abigail A ; Stanchak, Kathryn E ( June 2019 , Integrative and Comparative Biology)

   Abstract Modern computational and imaging methods are revolutionizing the fields of comparative morphology, biomechanics, and ecomorphology. In particular, imaging tools such as X-ray micro computed tomography (µCT) and diffusible iodine-based contrast enhanced CT allow observing and measuring small and/or otherwise inaccessible anatomical structures, and creating highly accurate three-dimensional (3D) renditions that can be used in biomechanical modeling and tests of functional or evolutionary hypotheses. But, do the larger datasets generated through 3D digitization always confer greater power to uncover functional or evolutionary patterns, when compared with more traditional methodologies? And, if so, why? Here, we contrast the advantages and challenges of using data generated via (3D) CT methods versus more traditional (2D) approaches in the study of skull macroevolution and feeding functional morphology in bats. First, we test for the effect of dimensionality and landmark number on inferences of adaptive shifts during cranial evolution by contrasting results from 3D versus 2D geometric morphometric datasets of bat crania. We find sharp differences between results generated from the 3D versus some of the 2D datasets (xy, yz, ventral, and frontal), which appear to be primarily driven by the loss of critical dimensions of morphological variation rather than number of landmarks. Second, we examine differences in accuracy and precision among 2D and 3D predictive models of bite force by comparing three skull lever models that differ in the sources of skull and muscle anatomical data. We find that a 3D model that relies on skull µCT scans and muscle data partly derived from diceCT is slightly more accurate than models based on skull photographs or skull µCT and muscle data fully derived from dissections. However, the benefit of using the diceCT-informed model is modest given the effort it currently takes to virtually dissect muscles from CT scans. By contrasting traditional and modern tools, we illustrate when and why 3D datasets may be preferable over 2D data, and vice versa, and how different methodologies can complement each other in comparative analyses of morphological function and evolution. 

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