scholarly journals Superimposition of 3D maxillary digital models using open-source software

2019 ◽  
Vol 24 (2) ◽  
pp. 81-91 ◽  
Author(s):  
Murilo Augusto Anacleto ◽  
Bernardo Quiroga Souki
Keyword(s):  
Open Source ◽  
Outcome Assessment ◽  
Open Source Software ◽  
Clinical Case ◽  
Three Dimensional ◽  
Digital Tools ◽  
3D Analysis ◽  
Two Dimensional ◽  
Digital Models ◽  
Dentofacial Orthopedics

Abstract Historically, whether for research purposes or clinical monitoring, orthodontic evaluation of dental movements has been done using plaster study models and two dimensional (2D) radiographs. However, new frontiers for the diagnosis, planning and outcome assessment of orthodontic treatments have arisen, due to the revolutionary digital tools which enable a three dimensional (3D) computerized analysis of dental movements by means of digital models. However, the software for 3D analysis are often costly, resulting in limited access to orthodontists. The present study aims to describe, through a clinical case presented to the Brazilian Board of Orthodontics and Dentofacial Orthopedics, a method for the superimposition of maxillary digital models using an open-source software to evaluate dental movements.

Demonstration of an Aerodynamic Design Process for Turbomachines Using Open Source Software Tools

2010 ◽  
Author(s):  
Oliver Borm ◽  
Balint Balassa ◽  
Sebastian Barthmes ◽  
Julius Fellerhoff ◽  
Andreas Ku¨hrmann ◽  
...  
Keyword(s):  
Open Source ◽  
Design Process ◽  
Open Source Software ◽  
Compressible Flows ◽  
Three Dimensional ◽  
Axial Compressor ◽  
Software Tools ◽  
Two Dimensional ◽  
Aerodynamic Design ◽  
Student Projects

This paper demonstrates an aerodynamic design process for turbomachines for compressible flows, using exclusively open source software tools. Some relevant software already existed and few additional components were required, which have been developed mainly by students and are available at ftp.lfa.mw.tum.de. The geometry of turbomachine blades is described with a newly developed NURBS based blade designer. One-dimensional preliminary analysis is done with OpenOffice.org Calc and an extended mean line program, where loss models are already included. For two-dimensional through-flow computations a compressible streamline curvature method was implemented. Two-dimensional blade-to-blade and three-dimensional simulations are performed with the CFD toolbox OpenFOAM. The two- and three-dimensional results are visualized and analyzed using the open source postprocessing tool ParaView. The presented tools are regularly used in student projects. A generic one stage axial compressor was created with the workflow as a showcase in order to demonstrate the capabilities of the open source software tools.

scholarly journals PhytoSFDM version 1.0.0: Phytoplankton Size and Functional Diversity Model

2016 ◽  
Vol 9 (11) ◽  
pp. 4071-4085 ◽  
Author(s):  
Esteban Acevedo-Trejos ◽  
Gunnar Brandt ◽  
S. Lan Smith ◽  
Agostino Merico
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Marine Ecosystem ◽  
Three Dimensional ◽  
Functional Trait ◽  
Global Ocean ◽  
Total Biomass ◽  
Spatially Resolved ◽  
Phytoplankton Communities ◽  
Natural Complexity

Abstract. Biodiversity is one of the key mechanisms that facilitate the adaptive response of planktonic communities to a fluctuating environment. How to allow for such a flexible response in marine ecosystem models is, however, not entirely clear. One particular way is to resolve the natural complexity of phytoplankton communities by explicitly incorporating a large number of species or plankton functional types. Alternatively, models of aggregate community properties focus on macroecological quantities such as total biomass, mean trait, and trait variance (or functional trait diversity), thus reducing the observed natural complexity to a few mathematical expressions. We developed the PhytoSFDM modelling tool, which can resolve species discretely and can capture aggregate community properties. The tool also provides a set of methods for treating diversity under realistic oceanographic settings. This model is coded in Python and is distributed as open-source software. PhytoSFDM is implemented in a zero-dimensional physical scheme and can be applied to any location of the global ocean. We show that aggregate community models reduce computational complexity while preserving relevant macroecological features of phytoplankton communities. Compared to species-explicit models, aggregate models are more manageable in terms of number of equations and have faster computational times. Further developments of this tool should address the caveats associated with the assumptions of aggregate community models and about implementations into spatially resolved physical settings (one-dimensional and three-dimensional). With PhytoSFDM we embrace the idea of promoting open-source software and encourage scientists to build on this modelling tool to further improve our understanding of the role that biodiversity plays in shaping marine ecosystems.

scholarly journals In-House, Open-Source 3D-Software-Based, CAD/CAM-Planned Mandibular Reconstructions in 20 Consecutive Free Fibula Flap Cases: An Explorative Cross-Sectional Study With Three-Dimensional Performance Analysis

2021 ◽  
Vol 11 ◽  
Author(s):  
Lucas M. Ritschl ◽  
Paul Kilbertus ◽  
Florian D. Grill ◽  
Matthias Schwarz ◽  
Jochen Weitz ◽  
...  
Keyword(s):  
Open Source ◽  
Dimensional Analysis ◽  
Open Source Software ◽  
Three Dimensional ◽  
Cross Sectional Study ◽  
Sectional Study ◽  
Free Fibula Flap ◽  
Cross Sectional ◽  
Cad Cam ◽  
Free Fibula

BackgroundMandibular reconstruction is conventionally performed freehand, CAD/CAM-assisted, or by using partially adjustable resection aids. CAD/CAM-assisted reconstructions are usually done in cooperation with osteosynthesis manufacturers, which entails additional costs and longer lead time. The purpose of this study is to analyze an in-house, open-source software-based solution for virtual planning.Methods and MaterialsAll consecutive cases between January 2019 and April 2021 that underwent in-house, software-based (Blender) mandibular reconstruction with a free fibula flap (FFF) were included in this cross-sectional study. The pre- and postoperative Digital Imaging and Com munications in Medicine (DICOM) data were converted to standard tessellation language (STL) files. In addition to documenting general information (sex, age, indication for surgery, extent of resection, number of segments, duration of surgery, and ischemia time), conventional measurements and three-dimensional analysis methods (root mean square error [RMSE], mean surface distance [MSD], and Hausdorff distance [HD]) were used.ResultsTwenty consecutive cases were enrolled. Three-dimensional analysis of preoperative and virtually planned neomandibula models was associated with a median RMSE of 1.4 (0.4–7.2), MSD of 0.3 (-0.1–2.9), and HD of 0.7 (0.1–3.1). Three-dimensional comparison of preoperative and postoperative models showed a median RMSE of 2.2 (1.5–11.1), MSD of 0.5 (-0.6–6.1), and HD of 1.5 (1.1–6.5) and the differences were significantly different for RMSE (p < 0.001) and HD (p < 0.001). The difference was not significantly different for MSD (p = 0.554). Three-dimensional analysis of virtual and postoperative models had a median RMSE of 2.3 (1.3–10.7), MSD of -0.1 (-1.0–5.6), and HD of 1.7 (0.1–5.9).ConclusionsOpen-source software-based in-house planning is a feasible, inexpensive, and fast method that enables accurate reconstructions. Additionally, it is excellent for teaching purposes.

Visualizing the Bug Distribution Information Available in Software Bug Repositories

2014 ◽  
pp. 48-66
Author(s):  
N. K. Nagwani ◽  
S. Verma
Keyword(s):  
Open Source ◽  
Three Dimensional ◽  
Distribution Patterns ◽  
Two Dimensional ◽  
Software Bugs ◽  
Process Visualization ◽  
Software Information ◽  
Visualization Techniques ◽  
Software Bug ◽  
Bug Repositories

Software repositories contain a wealth of information that can be analyzed for knowledge extraction. Software bug repositories are one such repository that stores the information about the defects identified during the development of software. Information available in software bug repositories like number of bugs priority-wise, component-wise, status-wise, developers-wise, module-wise, summary-terms-wise, can be visualized with the help of two- or three-dimensional graphs. These visualizations help in understanding the bug distribution patterns, software matrices related to the software bugs, and developer information in the bug-fixing process. Visualization techniques are exploited with the help of open source technologies in this chapter to visualize the bug distribution information available in the software bug repositories. Two-dimensional and three-dimensional graphs are generated using java-based open source APIs, namely Jzy3d (Java Easy 3d) and JFreeChart. Android software bug repository is selected for the experimental demonstrations of graphs. The textual bug attribute information is also visualized using frequencies of frequent terms present in it.

scholarly journals Software-Based Three-Dimensional Deconvolution Microscopy of Cytoskeletal Proteins in Cultured Fibroblast Using Open-Source Software and Open Hardware

2019 ◽  
Vol 5 (12) ◽  
pp. 88
Author(s):  
Kazuo Katoh
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Laser Scanning ◽  
Low Cost ◽  
Three Dimensional ◽  
Cytoskeletal Proteins ◽  
Laser Scanning Microscopy ◽  
Confocal Laser ◽  
Actual Measurement ◽  
Open Hardware

As conventional fluorescence microscopy and confocal laser scanning microscopy generally produce images with blurring at the upper and lower planes along the z-axis due to non-focal plane image information, the observation of biological images requires “deconvolution.” Therefore, a microscope system’s individual blur function (point spread function) is determined theoretically or by actual measurement of microbeads and processed mathematically to reduce noise and eliminate blurring as much as possible. Here the author describes the use of open-source software and open hardware design to build a deconvolution microscope at low cost, using readily available software and hardware. The advantage of this method is its cost-effectiveness and ability to construct a microscope system using commercially available optical components and open-source software. Although this system does not utilize expensive equipment, such as confocal and total internal reflection fluorescence microscopes, decent images can be obtained even without previous experience in electronics and optics.

scholarly journals Computational generation of an annotated gigalibrary of synthesizable, composite peptidic macrocycles

2020 ◽  
Vol 117 (40) ◽  
pp. 24679-24690
Author(s):  
Ishika Saha ◽  
Eric K. Dang ◽  
Dennis Svatunek ◽  
Kendall N. Houk ◽  
Patrick G. Harran
Keyword(s):  
Virtual Screening ◽  
Open Source ◽  
Open Source Software ◽  
Large Scale ◽  
Three Dimensional ◽  
Pharmacological Properties ◽  
Robust Methods ◽  
Small Peptide ◽  
Multistep Reaction ◽  
Condensed Heterocycles

Peptidomimetic macrocycles have the potential to regulate challenging therapeutic targets. Structures of this type having precise shapes and drug-like character are particularly coveted, but are relatively difficult to synthesize. Our laboratory has developed robust methods that integrate small-peptide units into designed scaffolds. These methods create macrocycles and embed condensed heterocycles to diversify outcomes and improve pharmacological properties. The hypothetical scope of the methodology is vast and far outpaces the capacity of our experimental format. We now describe a computational rendering of our methodology that creates an in silico three-dimensional library of composite peptidic macrocycles. Our open-source platform, CPMG (Composite Peptide Macrocycle Generator), has algorithmically generated a library of 2,020,794,198 macrocycles that can result from the multistep reaction sequences we have developed. Structures are generated based on predicted site reactivity and filtered on the basis of physical and three-dimensional properties to identify maximally diverse compounds for prioritization. For conformational analyses, we also introduce ConfBuster++, an RDKit port of the open-source software ConfBuster, which allows facile integration with CPMG and ready parallelization for better scalability. Our approach deeply probes ligand space accessible via our synthetic methodology and provides a resource for large-scale virtual screening.

Virtual Reconstruction as Archaeological Observation: Embracing New Ways of Treating Sites, Places and Landscapes

2019 ◽  
Vol 7 (2) ◽  
pp. 127-139 ◽  
Author(s):  
Matthew J. Douglass ◽  
Zachary R. Day ◽  
Jeremy C. Brunette ◽  
Peter Bleed ◽  
Douglas Scott
Keyword(s):  
Open Source ◽  
Case Studies ◽  
Open Source Software ◽  
The Other ◽  
Digital Tools ◽  
Archaeological Heritage ◽  
Common Heritage ◽  
Online Tutorials ◽  
Virtual Reconstruction ◽  
Southern Oklahoma

AbstractVirtual Reconstruction is a powerful tool broadly suited to a diverse array of archaeological heritage applications. In practice, however, reconstruction has largely focused on grand and monumental sites. Here we present two case studies–one from southern Oklahoma, the other from western Nebraska–to explore the use of this technology for more common heritage applications. The goal of this article is to advertise the dilemma we faced with communicating information on ephemeral sites and how we, as nonspecialists, solved the issue using affordable and accessible digital tools. Our workflow makes use of common tools (GIS) and open source software and online tutorials provide step by step instruction to support its replication. In presenting our experiences and the results of these efforts, we hope to spur similar applications in the use of Virtual Reconstruction to communicate information on archaeological heritage more broadly.

Contact Temperature in Dry Bearings. Three Dimensional Theory and Verification

1981 ◽  
Vol 103 (2) ◽  
pp. 243-251 ◽  
Author(s):  
A. Floquet ◽  
D. Play
Keyword(s):  
Fourier Transform ◽  
Boundary Conditions ◽  
Experimental Verification ◽  
Three Dimensional ◽  
Contact Temperature ◽  
3D Analysis ◽  
New Work ◽  
Two Dimensional ◽  
Dimensional Theory ◽  
Infra Red

Boundary conditions were arbitrarily specified in an earlier two dimensional (2D) analysis of contact temperature. In this new work a general three dimensional (3D) Fourier transform solution is obtained from which for specific cases, the boundary conditions can be estimated. Further, experimental verification of 3D analysis was performed using infra-red technique.

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