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

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.

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 3DWofE: An open-source software package for three-dimensional weights of evidence modeling

2020 ◽  
Vol 6 ◽  
pp. 100039
Author(s):  
Ehsan Farahbakhsh ◽  
Ardeshir Hezarkhani ◽  
Taymour Eslamkish ◽  
Abbas Bahroudi ◽  
Rohitash Chandra
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Package ◽  
Three Dimensional ◽  
Weights Of Evidence ◽  
Open Source Software Package

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.

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.

SCILAB-Based Robust Control Design and Analysis for an Aerospace System

2013 ◽  
Vol 390 ◽  
pp. 454-458
Author(s):  
Yoon Soo Kim
Keyword(s):  
Robust Control ◽  
Open Source ◽  
Software Package ◽  
Control Design ◽  
Aerospace Engineering ◽  
Free Software ◽  
Main Motivation ◽  
Robust Control Design

This paper presents a SCILAB-based robust control and analysis example from aerospace engineering. The main motivation of this work is the lack of documentation for advanced users of SCILAB. Using the programming ideas developed for basic robust control and analysis in [1], a practical example from aerospace engineering is shown to demonstrate the merit of an open-source free software package, SCILAB.

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.

scholarly journals DRRGenerator: A Three-dimensional Slicer Extension for the Rapid and Easy Development of Digitally Reconstructed Radiographs

2020 ◽  
Vol 10 ◽  
pp. 69
Author(s):  
Lance Levine ◽  
Marc Levine
Keyword(s):  
Open Source ◽  
Three Dimensional ◽  
Clinical Information ◽  
X Rays ◽  
3D Slicer ◽  
X Ray ◽  
Medical Interventions ◽  
Digitally Reconstructed Radiographs ◽  
Imaging Application ◽  
Ct Data

As the interest in image-guided medical interventions has increased, so too has the necessity for open-source software tools to provide the required capabilities without exorbitant costs. A common issue encountered in these procedures is the need to compare computed tomography (CT) data with X-ray data, for example, to compare pre-operative CT imaging with intraoperative X-rays. A software approach to solve this dilemma is the production of digitally reconstructed radiographs (DRRs) which computationally simulate an X-ray-type image from CT data. The resultant image can be easily compared to an X-ray image and can provide valuable clinical information, such as small anatomical changes that have occurred between the pre-operative and operative imaging (i.e., vertebral positioning). To provide an easy way for clinicians to make their own DRRs, we propose DRR generator, a customizable extension for the open-source medical imaging application three-dimensional (3D) Slicer. DRR generator provides rapid computation of DRRs through a highly customizable user interface. This extension provides end-users a free, open-source, and reliable way of generating DRRs. This program is integrated within 3D Slicer and thus can utilize its powerful imaging tools to provide a comprehensive segmentation and registration application for clinicians and researchers. DRR generator is available for download through 3D Slicer’s in-app extension manager and requires no additional software.

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