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The Natural Historian's Guide to the CT Galaxy: Step-by-Step Instructions for Preparing and Analyzing Computed Tomographic (CT) Data Using Cross-Platform, Open Access Software.

ABSTRACT: The decreasing cost of acquiring computed tomographic (CT) data has fueled a global effort to digitize the anatomy of museum specimens. This effort has produced a wealth of open access digital three-dimensional (3D) models of anatomy available to anyone with access to the Internet. The potential applications of these data are broad, ranging from 3D printing for purely educational purposes to the development of highly advanced biomechanical models of anatomical structures. However, while virtually anyone can access these digital data, relatively few have the training to easily derive a desirable product (e.g., a 3D visualization of an anatomical structure) from them. Here, we present a workflow based on free, open source, cross-platform software for processing CT data. We provide step-by-step instructions that start with acquiring CT data from a new reconstruction or an open access repository, and progress through visualizing, measuring, landmarking, and constructing digital 3D models of anatomical structures. We also include instructions for digital dissection, data reduction, and exporting data for use in downstream applications such as 3D printing. Finally, we provide Supplementary Videos and workflows that demonstrate how the workflow facilitates five specific applications: measuring functional traits associated with feeding, digitally isolating anatomical structures, isolating regions of interest using semi-automated segmentation, collecting data with simple visual tools, and reducing file size and converting file type of a 3D model.

SUBMITTER: Buser TJ

PROVIDER: S-EPMC7671151 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Aim:To evaluate the performance of three contrast media (CM) injection protocols for cardiac computed tomography angiography (CCTA) based on body weight (BW), lean BW (LBW), and cardiac output (CO). Materials and methods. A total of 327 consecutive patients referred for CCTA were randomized into one of the three CM injection protocols, where CM injection was based on either BW (112 patients), LBW (108 patients), or CO (107 patients). LBW and CO were calculated via formulas. All scans were ECG-gated and performed on a third-generation dual-source CT with 70-120?kV (automated tube voltage selection) and 100?kVqual.ref/330?mAsqual.ref. CM injection protocols were also adapted to scan time and tube voltage. The primary outcome was the proportion of patients with optimal intravascular attenuation (325-500?HU). Secondary outcomes were mean and standard deviation of intravascular attenuation values (HU), contrast-to-noise ratio (CNR), and subjective image quality with a 4-point Likert scale (1?=?poor/2?=?sufficient/3?=?good/4?=?excellent). The t-test for independent samples was used for pairwise comparisons between groups, and a chi-square test (?2) was used to compare categorical variables between groups. All p values were 2-sided, and a p < 0.05 was considered statistically significant. Results:Mean overall HU and CNR were 423?±?60HU/14?±?3 (BW), 404?±?62HU/14?±?3 (LBW), and 413?±?63HU/14?±?3 (CO) with a significant difference between groups BW and LBW (p=0.024). The proportion of patients with optimal intravascular attenuation (325-500?HU) was 83.9%, 84.3%, and 86.9% for groups BW, LBW, and CO, respectively, and between-group differences were small and nonsignificant. Mean CNR was diagnostic (?10) in all groups. The proportion of scans with good-excellent image quality was 94.6%, 86.1%, and 90.7% in the BW, LBW, and CO groups, respectively. The difference between proportions was significant between the BW and LBW groups. Conclusion:Personalization of CM injection protocols based on BW, LBW, and CO, and scan time and tube voltage in CCTA resulted in low variation between patients in terms of intravascular attenuation and a high proportion of scans with an optimal intravascular attenuation. The results suggest that personalized CM injection protocols based on LBW or CO have no additional benefit when compared with CM injection protocols based on BW.

Dataset Information

The Natural Historian's Guide to the CT Galaxy: Step-by-Step Instructions for Preparing and Analyzing Computed Tomographic (CT) Data Using Cross-Platform, Open Access Software.

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