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opencc-by-4.0Apr 2020View details →

Hydrate spatial distribution influence on the mechanical behavior hydrate-bearing sediment using computed tomography

This supporting information includes two Movie S1-2, illustrating the deformation evolution of the specimen # O-1 and specimen # O-2. Movie S1 is uploaded with file name Movie S1.gif. Detailed information includes the deformation evolution of the specimen # O-1. Movie S2 is uploaded with file name Movie S2. gif. Detailed information includes the deformation evolution of the specimen # O-2.

opencc-by-4.0May 2020View details →

Noise study data for: Mechanisms of root-reinforcement in soils: an experimental methodology using four-dimensional X-ray computed tomography and digital volume correlation

This dataset contains noise study data used in the paper: Mechanisms of root-reinforcement in soils: an experimental methodology using four-dimensional X-ray computed tomography and digital volume correlation. These include raw CT scans and processed digital volume correlation data. This dataset is part of another dataset which covers other aspects of the paper DOI: <a href="http://www.doi.org/10.5281/zenodo.3352268">10.5281/zenodo.3352268</a> The structure of the dataset is as follows: <ul> <li>Noise study CT raw volumes are contained in a zip file. There are four raw files corresponding to the four noise study steps. These files are 8-bit unsigned, dimensions are 1800 x 1800 x 1400 pixels. A txt file giving more details to the data is included. <ul> <li>CT_Raw_data_Noise_Scans.zip</li> </ul> </li> <li>Metadata files generated for each scan given details of scan parameters are found in the zip file: <ul> <li>CT_Scan_Metadata.zip</li> </ul> </li> <li>Tabulated digital volume data for the noise study scans are contained in the zip file. Tabulated data for each subset size is included in subfolders. A .txt file explains the structure of the tab separated .dat files, i.e. what each column of data represents, and what CT scan each of the four .dat files relate to. <ul> <li>DVC_Noise_Study_Data.zip</li> </ul> </li> </ul>

opencc-zeroDec 2019View details →

Data from: Automatic segmentation of multiple cardiovascular structures from cardiac computed tomography angiography images using deep learning

Objectives: To develop, demonstrate and evaluate an automated deep learning method for multiple cardiovascular structure segmentation. Background: Segmentation of cardiovascular images is resource-intensive. We design an automated deep learning method for the segmentation of multiple structures from Coronary Computed Tomography Angiography (CCTA) images. Methods: Images from a multicenter registry of patients that underwent clinically-indicated CCTA were used. The proximal ascending and descending aorta (PAA, DA), superior and inferior vena cavae (SVC, IVC), pulmonary artery (PA), coronary sinus (CS), right ventricular wall (RVW) and left atrial wall (LAW) were annotated as ground truth. The U-net-derived deep learning model was trained, validated and tested in a 70:20:10 split. Results: The dataset comprised 206 patients, with 5.130 billion pixels. Mean age was 59.9 ± 9.4 yrs., and was 42.7% female. An overall median Dice score of 0.820 (0.782, 0.843) was achieved. Median Dice scores for PAA, DA, SVC, IVC, PA, CS, RVW and LAW were 0.969 (0.979, 0.988), 0.953 (0.955, 0.983), 0.937 (0.934, 0.965), 0.903 (0.897, 0.948), 0.775 (0.724, 0.925), 0.720 (0.642, 0.809), 0.685 (0.631, 0.761) and 0.625 (0.596, 0.749) respectively. Apart from the CS, there were no significant differences in performance between sexes or age groups. Conclusions: An automated deep learning model demonstrated segmentation of multiple cardiovascular structures from CCTA images with reasonable overall accuracy when evaluated on a pixel level.

opencc-by-4.0Jun 2020View details →

Petermann Fjord Sediment Core Computed Tomography (CT) Scans (Cruise OD1507)

Computed tomography (CT) scans of sediment cores collected from Petermann Fjord during the PETERMANN15 expedition of the Swedish Icebreaker Oden, OD1507.  Included cores, 03TC, 03PC, 04GC, 06PC, 08GC, 10PC, 10TC, 40PC, 40TC, and 41GC.  Data include 2 mm thick coronal slices in DICOM format and SedCT products, including images and CT numbers.

opencc-zeroAug 2020View details →

Predictors of abnormal computed tomography findings for paediatric head injury: a retrospective cohort study

Objectives: Head injuries in children are common causes for visits to the emergency department (ED). Computed tomography (CT) scans are useful for confirming head injury diagnoses. However, radiation exposure from CT scans might cause lethal malignancies. We aimed to examine predictors for the indication of performing CT scans necessary for diagnosis. Design: Retrospective cohort study. Setting: Three EDs in Japan Participants: Patients aged <16 years with head trauma who underwent CT. Primary and Secondary Outcome Measures: The primary outcome measure was abnormal CT findings that were evaluated using the area under the receiver-operating characteristic curve (AUC). We derived predictors from three existing CDRs: Canadian Assessment of Tomography for Childhood Head Injury (CATCH), Children's Head Injury Algorithm for the Prediction of Important Clinical Events (CHALICE), and Paediatric Emergency Care Applied Research Network (PECARN). Results: Of 1,103 eligible patients, 410 were included in this study. There were 283 (68%) boys, and the median age was 2 years. In total, 35 (9%) patients showed an abnormality, 73 (18%) were admitted, and 3 (0.7%) underwent neurosurgery. We developed a CDR consisting of 6 predictors for identifying children with abnormal CT findings: (1) severe or worsening headache; (2) GCS <15; (3) signs of skull fracture; (4) hematoma; (5) loss of consciousness; and (6) altered mental status. Our CDR had a sensitivity of 74.3%, a specificity of 75.2%, a negative predictive value of 96.9%, and a positive predictive value of 21.8%. The AUC for our rule was not inferior to those for CATCH, CHALICE, and PECARN {0.75 (95% confidence interval [CI], 0.67-0.81) versus 0.64 (95% CI, 0.56-0.73; p<0.05), 0.68 (95% CI, 0.60–0.76; p=0.28), and 0.67 (95% CI, 0.60-0.74); p=0.10}. Conclusions: Our findings suggest that a CDR, which lowers the frequency of CT in children with head injuries, must be developed and validated.

opencc-by-4.0Nov 2020View details →

Pitfalls of Computed Tomography 3D Reconstruction Models in Cranial Nonmetric Analysis

Many studies in the literature have highlighted the utility of virtual 3D databanks as a substitute for real skeletal collections and the important application of radiological records in personal identification. However, none have investigated the accuracy of virtual material compared to skeletal remains in nonmetric variant analysis using 3D models. The present study investigates the accuracy of 20 computed tomography (CT) 3D reconstruction models compared to the real crania, focusing on the quality of the reproduction of the real crania and the possibility to detect 29 dental/cranial morphological variations in 3D images. An interobserver analysis was performed to evaluate trait identification, number, position, and shape. Results demonstrate a false bone loss in 3D models in some cranial regions, specifically the maxillary and occipital bones in 85% and 20% of the samples. Additional analyses revealed several difficulties in the detection of cranial nonmetric traits in 3D models, resulting in incorrect identification in circa 70% of the traits. In particular, pitfalls included the detection of erroneous position, error in presence/absence rates, in number, and in shape. The lowest percentages of correct evaluations were found in traits localized in the lateral side of the cranium and for the infraorbital suture, mastoid foramen, and crenulation. The present study highlights important pitfalls in CT scan when compared with the real crania for nonmetric analysis. This may have crucial consequences in cases where 3D databanks are used as a source of reference population data for nonmetric traits and pathologies and during bone-CT comparisons for identification purposes.

Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"

Phase-contrast CT of BDL rats liver-8 week

Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"

Phase-contrast CT of BDL rats liver-6 week

Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"

Phase-contrast CT of BDL rats liver-control group

Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"

Phase-contrast CT of BDL rats liver-4 week

opencc-zeroDec 2014View details →

Data from: Computed tomography, anatomical description and three-dimensional reconstruction of the lower jaw of Eusthenopteron foordi Whiteaves, 1881 from the Upper Devonian of Canada

The cranial anatomy of the iconic early tetrapod Eusthenopteron foordi is probably the best understood of all fossil fishes. In contrast, the anatomy of the lower jaw – crucial for both phylogenetics and biomechanical analyses – has been only superficially described. Computed tomography data of three Eusthenopteron skulls were segmented using visualization software to digitally separate bone from matrix and individual bones from each other. Here, we present a new description of the lower jaw of Eusthenopteron based on microcomputed tomography data, including the following: detailed description of sutural morphology and the mandibular symphysis; confirmed occurrence of pre- and intercoronoid fossae on the dorsal aspect of the lower jaw; and the arrangement of the submandibular bones. Furthermore, we identify a novel dermal ossification, the postsymphysial, present on the anteromedial aspect of the lower jaw in Eusthenopteron and describe its distribution in other stem tetrapod taxa. Sutural morphology is used to infer load regimes and, along with overall skull and lower jaw morphology, suggests that Eusthenopteron may have used biting along with suction feeding to capture and consume large prey. Finally, visualization software was used to repair and reconstruct the lower jaw, resulting in a three-dimensional digital reconstruction.

opencc-zeroDec 2013View details →

Data from: X-Ray computed tomography of two mammoth calf mummies

Two female woolly mammoth neonates from permafrost in the Siberian Arctic are the most complete mammoth specimens known. Lyuba, found on the Yamal Peninsula, and Khroma, from northernmost Yakutia, died at ages of approximately one and two months, respectively. Both specimens were CT-scanned, yielding detailed information on the stage of development of their dentition and skeleton and insight into conditions associated with death. Both mammoths died after aspirating mud. Khroma's body was frozen soon after death, leaving her tissues in excellent condition, whereas Lyuba's body underwent postmortem changes that resulted in authigenic formation of nodules of the mineral vivianite associated with her cranium and within diaphyses of long bones. CT data provide the only comprehensive approach to mapping vivianite distribution. Three-dimensional modeling and measurement of segmented long bones permits comparison between these individuals and with previously recovered specimens. CT scans of long bones and foot bones show developmental features such as density gradients that reveal ossification centers. The braincase of Khroma was segmented to show the approximate morphology of the brain; its volume is slightly less (∼2,300 cm3) than that of neonate elephants (∼2,500 cm3). Lyuba's premaxillae are more gracile than those of Khroma, possibly a result of temporal and/or geographic variation but probably also reflective of their age difference. Segmentation of CT data and 3-D modeling software were used to produce models of teeth that were too complex for traditional molding and casting techniques.

opennotspecifiedDec 2007View details →

FIGURES 11–12 in First fossil Micropholcommatidae (Araneae), imaged in Eocene Paris amber using X-Ray Computed Tomography

FIGURES 11–12. Photographs of Cenotextricella simoni sp. nov. (male holotype, MNHN PA 327) using traditional light microscopy. (1) dorsal view; (2) ventral view. See Fig. 5 for scale.

opennotspecifiedDec 2007View details →

FIGURES 1–10 in First fossil Micropholcommatidae (Araneae), imaged in Eocene Paris amber using X-Ray Computed Tomography

FIGURES 1–10. VHR-CT scans of Cenotextricella simoni sp. nov. (male holotype, MNHN PA 327). (1) dorsal view; (2) ventral view; (3) anterior view; (4) posterior view; (5) lateral view; (6) lateral sectioned view; (7) right pedipalp dorsal view; (8) right pedipalp posterior view; (9) left pedipalp retrolateral view; (10) right pedipalp prolateral view. Abbreviations: ALE, anterior lateral eye; AME, anterior median eye; c, conductor; cy, cymbium; ds, dorsal abdominal scutum; e, embolus; fe, femur; mt/t, metatarsus/tarsus joint; pa, patella; PLE, posterior lateral eye; PME, posterior median eye; st, sternum; th, tibial hook; ti, tibia; vs, ventral abdominal scutum.

opennotspecifiedDec 2014View details →

FIGURE 2 in A new microhylid frog, genus Rhombophryne, from northeastern Madagascar, and a re-description of R. serratopalpebrosa using micro-computed tomography

FIGURE 2. Comparative osteology of Rhombophryne vaventy sp. nov. (ZSM 357/2005, left in all pairs), and Rhombophryne serratopalpebrosa (MNHN 1975.24, right in all pairs), scaled to be equal in size; see Supplementary Figure S1 for manipulable model and scale. a: spinal columns in dorsal view (A = Atlas, T = Thoracic Vertebra, L = Lumbar Vertebra, S = Sacrum, U = Urostyle); b: ilia in dorsal view, with arrows indicating the third lumbar vertebrae and anterior-most end of the ilia; c: hands in ventral view, with arrows indicating the prepollex; d: head in ventral view, with arrows indicating the postchoanal prevomerine palate; e: columellae in dorsal view.

opennotspecifiedDec 2014View details →

FIGURE 1. Holotype ZSM 357 in A new microhylid frog, genus Rhombophryne, from northeastern Madagascar, and a re-description of R. serratopalpebrosa using micro-computed tomography

FIGURE 1. Holotype ZSM 357/2005 (FGZC 2876) (a–b) and paratype UADBA uncatalogued (FGZC 2842) (c–d) of Rhombophryne vaventy sp. nov. in dorsolateral and ventral views. Inset in c depicts the superciliary spines of the paratype. Note the variance in length of these spines.

opennotspecifiedDec 2014View details →

FIGURE 3 in A new microhylid frog, genus Rhombophryne, from northeastern Madagascar, and a re-description of R. serratopalpebrosa using micro-computed tomography

FIGURE 3. Comparative skull osteology of Rhombophryne serratopalpebrosa (MNHN 1975.24, right in all pairs) and Rhombophryne vaventy sp. nov. (ZSM 357/2005, left in all pairs), scaled to be equal in size. a: lateral view; b: ventral view; c: dorsal view. Abbreviations: angspl = angulosplenial, col = columella, fpar = frontoparietal, max = maxillary, mmk = mentomeckelian bone, pmax = premaxilla, pro = prootic, prsph = parasphenoid, pter = pterygoid, pvom = prevomer, pvom/ neopl = prevomer/neopalatine (either fused or replaced), qj = quadratojugal, spheth = sphenethmoid, spmax = septomaxilla, sq = squamosal.

opennotspecifiedDec 2011View details →

FIGURES 8–21 in A new species of anapid spider (Araneae: Araneoidea, Anapidae) in Eocene Baltic amber, imaged using phase contrast X-ray computed micro-tomography

FIGURES 8–21. CT reconstructions of Balticoroma wheateri new species (male holotype, GPIH). (8) frontal view showing chelicerae and labral spur; (9) view of right pedipalp showing embolus; (10–14) various views of right metatarsus 1, showing y-shaped clasping structure; (15) anterior view of specimen showing the section taken through the chelicerae to produce the raw data slice in Figure 16; (16) raw data slice demonstrating that the chelicerae and clypeal extentions are clearly separated; (20–21) various views of the right pedipalp. C, chelicera; ce, clypeal extension; co, dorsal cymbial outgrowth; cy, cymbium; e, embolus; eb, embolic base; ec, embolic coil;?fc, functional conductor sensu Wunderlich (2004); ls, labral spur; t, tegulum.

opennotspecifiedDec 2011View details →

FIGURE 1 in A new species of anapid spider (Araneae: Araneoidea, Anapidae) in Eocene Baltic amber, imaged using phase contrast X-ray computed micro-tomography

FIGURE 1. Microphotograph of Balticoroma wheateri new species (male holotype, GPIH). Body length = 1.8 mm.