Dataset Information

A preclinical micro-computed tomography database including 3D whole body organ segmentations.

ABSTRACT: The gold-standard of preclinical micro-computed tomography (?CT) data processing is still manual delineation of complete organs or regions by specialists. However, this method is time-consuming, error-prone, has limited reproducibility, and therefore is not suitable for large-scale data analysis. Unfortunately, robust and accurate automated whole body segmentation algorithms are still missing. In this publication, we introduce a database containing 225 murine 3D whole body ?CT scans along with manual organ segmentation of most important organs including heart, liver, lung, trachea, spleen, kidneys, stomach, intestine, bladder, thigh muscle, bone, as well as subcutaneous tumors. The database includes native and contrast-enhanced, regarding spleen and liver, ?CT data. All scans along with organ segmentation are freely accessible at the online repository Figshare. We encourage researchers to reuse the provided data to evaluate and improve methods and algorithms for accurate automated organ segmentation which may reduce manual segmentation effort, increase reproducibility, and even reduce the number of required laboratory animals by reducing a source of variability and having access to a reliable reference group.

SUBMITTER: Rosenhain S

PROVIDER: S-EPMC6298256 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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A preclinical micro-computed tomography database including 3D whole body organ segmentations.

Rosenhain Stefanie S Magnuska Zuzanna A ZA Yamoah Grace G GG Rawashdeh Wa'el Al WA Kiessling Fabian F Gremse Felix F

Scientific data 20181218

The gold-standard of preclinical micro-computed tomography (μCT) data processing is still manual delineation of complete organs or regions by specialists. However, this method is time-consuming, error-prone, has limited reproducibility, and therefore is not suitable for large-scale data analysis. Unfortunately, robust and accurate automated whole body segmentation algorithms are still missing. In this publication, we introduce a database containing 225 murine 3D whole body μCT scans along with m ...[more]

PMID: 30561432

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Project description:This study used available or purchased equipment and an image reconstruction system developed by the college of dentistry to establish a basic self-assembled micro-computed tomography (micro-CT) system. Such a system would be suitable for teaching dental radiology to dental students. Specifically, it could help students to understand the principles governing dental cone-beam computed tomography (CBCT) and provide graduate students with a system for scanning small samples (e.g., individual teeth) during the early stages of research. The self-assembled micro-CT system was constructed using a portable dental X-ray tube, an intraoral digital X-ray detector, a high-precision rotation stage, related bracket accessories, and a notebook computer. Reconstructed images and three-dimensional models of the maxillary right third molar were produced using the self-assembled micro-CT system and an advanced commercially available micro-CT system (Skyscan 2211). Subsequently, the reconstructed images and 3D models produced using the two systems were compared by two senior dentists to determine whether considerable visual differences could be observed. Finally, the signal-to-noise ratio (SNR) was used for quantitative analysis and to compare the systems. Although the self-assembled micro-CT system produced image boundaries that were not as sharp as those of Skyscan 2211, the images were nonetheless remarkably similar. In addition, the two micro-CT systems produced 3D models that were almost identical in appearance and root canal shape. Quantitative analysis revealed that Skyscan 2211 had produced a SNR that was superior to that of the self-assembled micro-CT system, with the difference ranging from 36.77% to 136.22%; enamel, which has a higher density, exhibited lower SNR differences, whereas dentin, which has a lower density, exhibited higher SNR differences. The self-assembled micro-CT system with a resolution of 36 ?m was created using a portable dental X-ray tube and an intraoral digital X-ray detector. Although the scanning time was relatively long (~30 min to scan images of a tooth), the images were adequate in the preliminary stage of experiments. More importantly, students were afforded the opportunity to observe the process of assembling and disassembling each component of a micro-CT scanner and thereby achieve a more comprehensive understanding of the principles governing micro-CT and dental CBCT.

Dataset Information

A preclinical micro-computed tomography database including 3D whole body organ segmentations.

Publications

A preclinical micro-computed tomography database including 3D whole body organ segmentations.

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