Dataset Information

CroSSED sequence, a new tool for 3D processing in geosciences using the free software 3DSlicer.

ABSTRACT: The scientific application of 3D imaging has evolved significantly over recent years. These techniques make it possible to study internal features by non-destructive analysis. Despite its potential, the development of 3D imaging in the Geosciences is behind other fields due to the high cost of commercial software and the scarce free alternatives. Most free software was designed for the Health Sciences, and the pre-settled workflows are not suited to geoscientific materials. Thus, an outstanding challenge in the Geosciences is to define workflows using free alternatives for Computed Tomography (CT) data processing, promoting data sharing, reproducibility, and the development of specific extensions. We present CroSSED, a processing sequence for 3D reconstructions of CT data, using 3DSlicer, a popular application in medical imaging. Its usefulness is exemplified in the study of burrows that have low-density contrast with respect to the host sediment. For geoscientists who have access to CT data and wish to reconstruct 3D structures, this method offers a wide range of possibilities and contributes to open-science and applied CT studies.

SUBMITTER: Dorador J

PROVIDER: S-EPMC7429493 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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CroSSED sequence, a new tool for 3D processing in geosciences using the free software 3DSlicer.

Dorador Javier J Rodríguez-Tovar Francisco J FJ

Scientific data 20200814 1

The scientific application of 3D imaging has evolved significantly over recent years. These techniques make it possible to study internal features by non-destructive analysis. Despite its potential, the development of 3D imaging in the Geosciences is behind other fields due to the high cost of commercial software and the scarce free alternatives. Most free software was designed for the Health Sciences, and the pre-settled workflows are not suited to geoscientific materials. Thus, an outstanding ...[more]

PMID: 32796857

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Project description:The mitigation of diffuse sediment pollution requires reliable provenance information so that measures can be targeted. Sediment source fingerprinting represents one approach for supporting these needs, but recent methodological developments have resulted in an increasing complexity of data processing methods rendering the approach less accessible to non-specialists. A comprehensive new software programme (SIFT; SedIment Fingerprinting Tool) has therefore been developed which guides the user through critical data analysis decisions and automates all calculations. Multiple source group configurations and composite fingerprints are identified and tested using multiple methods of uncertainty analysis. This aims to explore the sediment provenance information provided by the tracers more comprehensively than a single model, and allows for model configurations with high uncertainties to be rejected. This paper provides an overview of its application to an agricultural catchment in the UK to determine if the approach used can provide a reduction in uncertainty and increase in precision. Five source group classifications were used; three formed using a k-means cluster analysis containing 2, 3 and 4 clusters, and two a-priori groups based upon catchment geology. Three different composite fingerprints were used for each classification and bi-plots, range tests, tracer variability ratios and virtual mixtures tested the reliability of each model configuration. Some model configurations performed poorly when apportioning the composition of virtual mixtures, and different model configurations could produce different sediment provenance results despite using composite fingerprints able to discriminate robustly between the source groups. Despite this uncertainty, dominant sediment sources were identified, and those in close proximity to each sediment sampling location were found to be of greatest importance. This new software, by integrating recent methodological developments in tracer data processing, guides users through key steps. Critically, by applying multiple model configurations and uncertainty assessment, it delivers more robust solutions for informing catchment management of the sediment problem than many previously used approaches.

Dataset Information

CroSSED sequence, a new tool for 3D processing in geosciences using the free software 3DSlicer.

Publications

CroSSED sequence, a new tool for 3D processing in geosciences using the free software 3DSlicer.

Similar Datasets

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