DicomAnnotator: a Configurable Open-Source Software Program for Efficient DICOM Image Annotation

Dong, Qifei; Luo, Gang; Haynor, David R.; O’Reilly, Martin; Linnau, Ken F.; Yaniv, Ziv; Jarvik, Jeffrey G.; Cross, Nathan M.

doi:10.1007/s10278-020-00370-w

Cited by 10 publications

(5 citation statements)

References 16 publications

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“…3 A). Possible directions for estimating three-dimensional spinal geometry in rodents include the use of generalizable annotation tools adapted to micro-CT data such as DicomAnnotator [ 65 ] or the development of 3D reconstruction methods similar to the ones used by clinicians [ 66 – 68 ]. We opted for a custom annotation-based solution tailored to our specific need, i.e., estimating three-dimensional spinal trajectories without reconstructing individual vertebrae.…”

Section: Discussionmentioning

confidence: 99%

SCO-spondin knockout mice exhibit small brain ventricles and mild spine deformation

Xu,

Dugué,

Cantaut-Belarif

et al. 2023

Fluids Barriers CNS

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Reissner’s fiber (RF) is an extracellular polymer comprising the large monomeric protein SCO-spondin (SSPO) secreted by the subcommissural organ (SCO) that extends through cerebrospinal fluid (CSF)-filled ventricles into the central canal of the spinal cord. In zebrafish, RF and CSF-contacting neurons (CSF-cNs) form an axial sensory system that detects spinal curvature, instructs morphogenesis of the body axis, and enables proper alignment of the spine. In mammalian models, RF has been implicated in CSF circulation. However, challenges in manipulating Sspo, an exceptionally large gene of 15,719 nucleotides, with traditional approaches has limited progress. Here, we generated a Sspo knockout mouse model using CRISPR/Cas9-mediated genome-editing. Sspo knockout mice lacked RF-positive material in the SCO and fibrillar condensates in the brain ventricles. Remarkably, Sspo knockout brain ventricle sizes were reduced compared to littermate controls. Minor defects in thoracic spine curvature were detected in Sspo knockouts, which did not alter basic motor behaviors tested. Altogether, our work in mouse demonstrates that SSPO and RF regulate ventricle size during development but only moderately impact spine geometry.

show abstract

Section: Discussionmentioning

confidence: 99%

SCO-spondin knockout mice exhibit small brain ventricles and mild spine deformation

Xu,

Dugué,

Cantaut-Belarif

et al. 2023

Fluids Barriers CNS

View full text Add to dashboard Cite

show abstract

“…3A). Possible directions for estimating three-dimensional spinal geometry in rodents include the use of generalizable annotation tools adapted to micro-CT data such as DicomAnnotator [65] or the development of 3D reconstruction methods similar to the ones used by clinicians [66][67][68]. We opted for a custom annotation-based solution tailored to our specific need, i.e., estimating three-dimensional spinal trajectories without reconstructing individual vertebrae.…”

Section: Discussionmentioning

confidence: 99%

SCO-spondin knockout mice exhibit small brain ventricles and mild spine deformation

Dugué

Cantaut-Belarif

et al. 2023

Preprint

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Reissner’s fiber (RF) is an extracellular polymer comprising the large monomeric protein SCO-spondin (SSPO) secreted by the subcommissural organ (SCO) that extends through cerebrospinal fluid (CSF)-filled ventricles into the central canal of the spinal cord. In zebrafish, RF and CSF-contacting neurons (CSF-cNs) form an axial sensory system that detects spinal curvature, instructs morphogenesis of the body axis, and enables proper alignment of the spine. In mammalian models, RF has been implicated in CSF circulation. However, challenges in manipulatingSspo, an exceptionally large gene of 15,719 nucleotides, with traditional approaches has limited progress. Here, we generated aSspoknockout mouse model using CRISPR/Cas9-mediated genome-editing.Sspoknockout mice lacked RF-positive material in the SCO and fibrillar condensates in the brain ventricles. Remarkably,Sspoknockout brain ventricle sizes were reduced compared to littermate controls. Minor defects in thoracic spine curvature were detected inSspoknockouts, which did not alter basic motor behaviors tested. Altogether, our work in mouse demonstrates that SSPO and RF regulate ventricle size during development but only moderately impact spine geometry.

show abstract

“…On each radiograph in the local dataset, we annotated each vertebral body's four corner points and severity of OCF using DicomAnnotator (38), an open-source annotation software. Multiple groups participated in the process of annotating the corner points of each vertebral body.…”

Section: Local Datasetmentioning

confidence: 99%

Generalizability of Deep Learning Classification of Spinal Osteoporotic Compression Fractures on Radiographs Using an Adaptation of the Modified-2 Algorithm-Based Qualitative Criteria

Dong,

Luo,

Lane

et al. 2023

Academic Radiology

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DicomAnnotator: a Configurable Open-Source Software Program for Efficient DICOM Image Annotation

Cited by 10 publications

References 16 publications

SCO-spondin knockout mice exhibit small brain ventricles and mild spine deformation

SCO-spondin knockout mice exhibit small brain ventricles and mild spine deformation

SCO-spondin knockout mice exhibit small brain ventricles and mild spine deformation

Generalizability of Deep Learning Classification of Spinal Osteoporotic Compression Fractures on Radiographs Using an Adaptation of the Modified-2 Algorithm-Based Qualitative Criteria

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