scholarly journals Three-dimensional semi-automated volumetric assessment of the pulp space of teeth following regenerative dental procedures

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Heeresh Shetty ◽  
Shishir Shetty ◽  
Adesh Kakade ◽  
Aditya Shetty ◽  
Mohmed Isaqali Karobari ◽  
...  
Keyword(s):  
Medical Imaging ◽  
Open Source ◽  
Three Dimensional ◽  
Volume Estimation ◽  
Permanent Teeth ◽  
3D Slicer ◽  
Link Type ◽  
Volumetric Assessment ◽  
Critical Measure ◽  
Significant Difference

AbstractThe volumetric change that occurs in the pulp space over time represents a critical measure when it comes to determining the secondary outcomes of regenerative endodontic procedures (REPs). However, to date, only a few studies have investigated the accuracy of the available domain-specialized medical imaging tools with regard to three-dimensional (3D) volumetric assessment. This study sought to compare the accuracy of two different artificial intelligence-based medical imaging programs namely OsiriX MD (v 9.0, Pixmeo SARL, Bernex Switzerland, https://www.osirix-viewer.com) and 3D Slicer (http://www.slicer.org), in terms of estimating the volume of the pulp space following a REP. An Invitro assessment was performed to check the reliability and sensitivity of the two medical imaging programs in use. For the subsequent clinical application, pre- and post-procedure cone beam computed tomography scans of 35 immature permanent teeth with necrotic pulp and periradicular pathosis that had been treated with a cell-homing concept-based REP were processed using the two biomedical DICOM software programs (OsiriX MD and 3D Slicer). The volumetric changes in the teeth’s pulp spaces were assessed using semi-automated techniques in both programs. The data were statistically analyzed using t-tests and paired t-tests (P = 0.05). The pulp space volumes measured using both programs revealed a statistically significant decrease in the pulp space volume following the REP (P < 0.05), with no significant difference being found between the two programs (P > 0.05). The mean decreases in the pulp space volumes measured using OsiriX MD and 3D Slicer were 25.06% ± 19.45% and 26.10% ± 18.90%, respectively. The open-source software (3D Slicer) was found to be as accurate as the commercially available software with regard to the volumetric assessment of the post-REP pulp space. This study was the first to demonstrate the step-by-step application of 3D Slicer, a user-friendly and easily accessible open-source multiplatform software program for the segmentation and volume estimation of the pulp spaces of teeth treated with REPs.

scholarly journals Three-dimensional Semi-Automated Volumetric Assessment of the Pulp Space of Teeth with Regenerative Dental Procedures

2021 ◽  
Author(s):  
Heeresh Shetty ◽  
Shishir Shetty ◽  
Adesh Kakade ◽  
Aditya Shetty ◽  
Mohmed Isaqali Karobari ◽  
...  
Keyword(s):  
Open Source ◽  
Three Dimensional ◽  
T Test ◽  
Volume Estimation ◽  
Permanent Teeth ◽  
3D Slicer ◽  
Volumetric Assessment ◽  
Critical Measure ◽  
Significant Difference ◽  
Space Volume

Abstract Volumetric change of the pulp space over time is a critical measure to determine the outcome of regenerative endodontic procedures (REP). There is a paucity in the literature on the accuracy of domain specialized medical imaging tools for three dimensional (3D) volumetric assessment. Thus, the aim of this study was to compare two different medical image computing platforms (OsiriX MD and 3D Slicer) to estimate the volume of pulp space post REP. Pre and post CBCT Scans of 35 immature permanent teeth (n = 35) with necrotic pulp and periradicular pathosis treated with a cell-homing concept-based REP were processed using two biomedical DICOM software programs: OsiriX MD (commercially available, FDA approved) 2) and 3D Slicer (open source). Volumetric changes in the pulp space were assessed using semi-automated techniques in both the programmes. The data were statistically analyzed using t-test and paired t-test (P = 0.05). The pulp space volume measured with both the programmes showed a statistically significant decrease in pulp space volume post REP (P < 0.05), with no significant difference between the two programmes (P > 0.05). The mean decrease in pulp space volume with OsiriX MD and 3D Slicer were 25.06% ± 19.45% and 26.10.% ± 18.90% respectively. The open-source software (3D Slicer) was as accurate as the commercially available software for the volumetric assessment of the pulp space post REP. This study demonstrates the step-by-step application of 3D Slicer, a user-friendly, easily accessible, open-source multiplatform software for the segmentation and volume estimation of the pulp-space of teeth treated with REP.

Open Source Applications for Image Visualization and Processing in Neuroimaging Training

2015 ◽  
pp. 1319-1332
Author(s):  
Juan A. Juanes ◽  
Pablo Ruisoto ◽  
Alberto Prats-Galino ◽  
Andrés Framiñán
Keyword(s):  
Magnetic Resonance ◽  
Medical Imaging ◽  
Open Source ◽  
Medical Images ◽  
Three Dimensional ◽  
Mr Images ◽  
Image Visualization ◽  
3D Slicer ◽  
Volumetric Reconstruction ◽  
Key Features

The aim of this paper is to demonstrate the major role and potential of three of the most powerful open source computerized tools for the advanced processing of medical images, in the study of neuroanatomy. DICOM images were acquired with radiodiagnostic equipment using 1.5 Tesla Magnetic Resonance (MR) images. Images were further processed using the following applications: first, OsiriXTM version 4.0 32 bits for OS; Second, 3D Slicer version 4.3; and finally, MRIcron, version 6. Advanced neuroimaging processing requires two key features: segmentation and three-dimensional or volumetric reconstruction. Examples of identification and reconstruction of some of the most complex neuroimaging elements such vascular ones and tractographies are included in this paper. The three selected applications represent some of the most versatile technologies within the field of medical imaging.

Open Source Applications for Image Visualization and Processing in Neuroimaging Training

2014 ◽  
Vol 7 (2) ◽  
pp. 75-87 ◽  
Author(s):  
Juan A. Juanes ◽  
Pablo Ruisoto ◽  
Alberto Prats-Galino ◽  
Andrés Framiñán
Keyword(s):  
Magnetic Resonance ◽  
Medical Imaging ◽  
Open Source ◽  
Medical Images ◽  
Three Dimensional ◽  
Mr Images ◽  
Image Visualization ◽  
3D Slicer ◽  
Volumetric Reconstruction ◽  
Key Features

The aim of this paper is to demonstrate the major role and potential of three of the most powerful open source computerized tools for the advanced processing of medical images, in the study of neuroanatomy. DICOM images were acquired with radiodiagnostic equipment using 1.5 Tesla Magnetic Resonance (MR) images. Images were further processed using the following applications: first, OsiriXTM version 4.0 32 bits for OS; Second, 3D Slicer version 4.3; and finally, MRIcron, version 6. Advanced neuroimaging processing requires two key features: segmentation and three-dimensional or volumetric reconstruction. Examples of identification and reconstruction of some of the most complex neuroimaging elements such vascular ones and tractographies are included in this paper. The three selected applications represent some of the most versatile technologies within the field of medical imaging.

scholarly journals Measuring Differential Volume Using the Subtraction Tool for Three-Dimensional Breast Volumetry: A Proof of Concept Study

2020 ◽  
pp. 155335062094556
Author(s):  
Faith Hyun Kyung Jeon ◽  
Michelle Griffin ◽  
Aurora Almadori ◽  
Jajini Varghese ◽  
Stephanie Bogan ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Computer Software ◽  
Patient Positioning ◽  
Volumetric Analysis ◽  
Volumetric Assessment ◽  
Alternative Approach ◽  
Significant Difference ◽  
Actual Volume ◽  
Novel Method ◽  
The Subject

Background. Three-dimensional (3D) photography provides a promising means of breast volumetry. Sources of error using a single-captured surface to calculate breast volume include inaccurate designation of breast boundaries and prediction of the invisible chest wall generated by computer software. An alternative approach is to measure differential volume using subtraction of 2 captured surfaces. Objectives. To explore 3D breast volumetry using the subtraction of superimposed images to calculate differential volume. To assess optimal patient positioning for accurate volumetric assessment. Methods. Known volumes of breast enhancers simulated volumetric changes to the breast (n = 12). 3D photographs were taken (3dMDtorso) with the subject positioned upright at 90° and posteriorly inclined at 30°. Patient position, breathing, distance and camera calibration were standardised. Volumetric analysis was performed using 3dMDvultus software. Results. A statistically significant difference was found between actual volume and measured volumes with subjects positioned at 90° ( P < .05). No statistical difference was found at 30° ( P = .078), but subsequent Bland–Altman analysis showed evidence of proportional bias ( P < .05). There was good correlation between measured and actual volumes in both positions (r = .77 and r = .85, respectively). Univariate analyses showed breast enhancer volumes of 195 mL and 295 mL to incur bias. The coefficient of variation was 5.76% for single observer analysis. Conclusion. Positioning the subject at a 30° posterior incline provides more accurate results from better exposure of the inferior breast. The subtraction tool is a novel method of measuring differential volume. Future studies should explore methodology for application into the clinical setting.

scholarly journals Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs

2021 ◽  
Author(s):  
Soohyun Lee ◽  
Carl Vitzthum ◽  
Burak H. Alver ◽  
Peter J. Park
Keyword(s):  
Quality Control ◽  
Open Source ◽  
Source Code ◽  
Three Dimensional ◽  
File Format ◽  
Interaction Data ◽  
Text File ◽  
Storage And Retrieval ◽  
Link Type ◽  
Efficient Storage

AbstractSummaryAs the amount of three-dimensional chromosomal interaction data continues to increase, storing and accessing such data efficiently becomes paramount. We introduce Pairs, a block-compressed text file format for storing paired genomic coordinates from Hi-C data, and Pairix, an open-source C application to index and query Pairs files. Pairix (also available in Python and R) extends the functionalities of Tabix to paired coordinates data. We have also developed PairsQC, a collapsible HTML quality control report generator for Pairs files.AvailabilityThe format specification and source code are available at https://github.com/4dn-dcic/pairix, https://github.com/4dn-dcic/Rpairix and https://github.com/4dn-dcic/[email protected] or [email protected]

scholarly journals SlicerDMRI: Diffusion MRI and Tractography Research Software for Brain Cancer Surgery Planning and Visualization

2020 ◽  
pp. 299-309 ◽  
Author(s):  
Fan Zhang ◽  
Thomas Noh ◽  
Parikshit Juvekar ◽  
Sarah F. Frisken ◽  
Laura Rigolo ◽  
...  
Keyword(s):  
Open Source ◽  
Diffusion Tensor ◽  
Intraoperative Imaging ◽  
Time Integration ◽  
Three Dimensional ◽  
High Grade Glioma ◽  
Patient Specific ◽  
Imaging Data ◽  
3D Slicer ◽  
Research Software

PURPOSE We present SlicerDMRI, an open-source software suite that enables research using diffusion magnetic resonance imaging (dMRI), the only modality that can map the white matter connections of the living human brain. SlicerDMRI enables analysis and visualization of dMRI data and is aimed at the needs of clinical research users. SlicerDMRI is built upon and deeply integrated with 3D Slicer, a National Institutes of Health–supported open-source platform for medical image informatics, image processing, and three-dimensional visualization. Integration with 3D Slicer provides many features of interest to cancer researchers, such as real-time integration with neuronavigation equipment, intraoperative imaging modalities, and multimodal data fusion. One key application of SlicerDMRI is in neurosurgery research, where brain mapping using dMRI can provide patient-specific maps of critical brain connections as well as insight into the tissue microstructure that surrounds brain tumors. PATIENTS AND METHODS In this article, we focus on a demonstration of SlicerDMRI as an informatics tool to enable end-to-end dMRI analyses in two retrospective imaging data sets from patients with high-grade glioma. Analyses demonstrated here include conventional diffusion tensor analysis, advanced multifiber tractography, automated identification of critical fiber tracts, and integration of multimodal imagery with dMRI. RESULTS We illustrate the ability of SlicerDMRI to perform both conventional and advanced dMRI analyses as well as to enable multimodal image analysis and visualization. We provide an overview of the clinical rationale for each analysis along with pointers to the SlicerDMRI tools used in each. CONCLUSION SlicerDMRI provides open-source and clinician-accessible research software tools for dMRI analysis. SlicerDMRI is available for easy automated installation through the 3D Slicer Extension Manager.

scholarly journals SurfStamp: 3D Printer Compatible Molecular Surface Representation

2020 ◽  
Author(s):  
Toshiyuki Oda
Keyword(s):  
Open Source ◽  
Source Code ◽  
3D Structure ◽  
Three Dimensional ◽  
Molecular Surface ◽  
3D Printer ◽  
3D Object ◽  
Link Type ◽  
Surface Models ◽  
Version 2.0

AbstractSurfStamp is an application that is used to generate textures for surface models of proteins. The textures contain information about surface residues and the information is drawn directly on the 3D object of the models. This approach is more intuitive than the labeling functions that most three-dimensional (3D) structure viewers use to show residue information. Therefore, the use of this application enables researchers, readers, or audiences to easily determine which residues are contributing the surface they are focusing on.AvailabilityThe application is provided under the open-source Apache License Version 2.0 (http://www.apache.org/licenses/LICENSE-2.0). The application and source code are available from https://github.com/yamule/SurfStamp-public/releases.

scholarly journals Two-dimensional ultrasound: can it replace computed tomography in liver volume assessment?

2019 ◽  
Vol 50 (1) ◽  
Author(s):  
Shimaa Farghaly ◽  
Marwa Makboul ◽  
Mahmoud Refaat Shehata
Keyword(s):  
Computed Tomography ◽  
Gold Standard ◽  
Preoperative Evaluation ◽  
Liver Volume ◽  
Age Groups ◽  
Volume Measurement ◽  
Volume Estimation ◽  
Two Dimensional ◽  
Volumetric Assessment ◽  
Significant Difference

Abstract Background Liver volume estimation is considered as an integral part in preoperative evaluation in patients undergoing liver transplantation; computed tomography and magnetic resonance imaging are considered the gold standard methods for liver volume estimation, and both are reliable and valid in determination of liver volume via manual and semi-automated methods. Reliable and accurate set of three simple measurement planes using two-dimensional ultrasound for volumetric assessment of liver was determined, and predictive equation using these three simple measurements was performed, which is simple to perform and easy to calculate, in order to evaluate liver volume and validate these measurements against CT images. Our aim in this study was to evaluate the efficacy and validity of two-dimensional ultrasound in liver volume estimation compared to CT volumetry as a gold standard. Results A strong linear positive correlation with no statistical significant difference was found between 2D US and semi-automated CT volumetric, and result was r = 0.7402 and p > 0.05, with an average liver volume of 1572.10 (± 326.43) cm3 and 1559.30 (± 381.02) cm3 respectively. No statistically significant difference was found also between the two modalities in different age groups and different sexes. Conclusion Simple linear two-dimensional ultrasound could be considered an efficient, accurate, and trustable tool for liver volume measurement in clinical practice.

scholarly journals Three-dimensional volumetric rendition of cannon ball pulmonary metastases by the use of 3D Slicer, an open source free software package

2013 ◽  
Vol 2013 (feb04 1) ◽  
pp. bcr2012008248-bcr2012008248 ◽  
Author(s):  
S. Revannasiddaiah ◽  
S. P. Susheela ◽  
N. Madhusudhan ◽  
G. J. Mallarajapatna
Keyword(s):  
Open Source ◽  
Software Package ◽  
Pulmonary Metastases ◽  
Three Dimensional ◽  
Free Software ◽  
3D Slicer

scholarly journals Retrospective study on three-dimensional characteristics of mesiodens using CBCT in pediatric dentistry

2021 ◽  
Vol 48 (1) ◽  
pp. 77-94
Author(s):  
GiYoun Ryu ◽  
Ji-Soo Song ◽  
Teo Jeon Shin ◽  
Hong-Keun Hyun ◽  
Jung-Wook Kim ◽  
...  
Keyword(s):  
Treatment Plan ◽  
Three Dimensional ◽  
Pediatric Dentistry ◽  
Horizontal Direction ◽  
Permanent Teeth ◽  
Vertical Position ◽  
Factors Affecting ◽  
Significant Difference ◽  
National University ◽  
Seoul National University

The purpose of this study was to investigate the three-dimensional characteristics of mesiodens using Cone-beam Computed Tomography(CBCT) and analyze the factors affecting complications and anesthetic methods of extraction. This study evaluated 602 mesiodens of 452 patients who underwent extraction of mesiodens at the department of Pediatric Dentistry in Seoul National University Dental Hospital between 2017 and 2019.The ratio of mesiodens patients over total patient per year was gradually increased over the past 20 years. Mesiodens with labio-palatally horizontal direction while root directing labial were the most common among the mesiodens with horizontal direction. Mesiodens were the most common at the cervical side of the adjacent teeth(37.0%) and mesiodens located in the near-palatal side were observed about 3.83 times higher than the far-palatal side. Most of the mesiodens(82.1%) were in contact with adjacent permanent teeth on all three sides of the CBCT and 46.2% of mesiodens had curved roots. The patient’s age, vertical position, presence of complications, and proximity showed a significant difference in the selection of general anesthesia among anesthetic methods. The direction and vertical position of mesiodens had a significant effect on complications.These results provide a better understanding of mesiodens for establishing an accurate diagnosis and treatment plan.

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